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#\#CIF_2.0
#\#STAR
##########################################################################
# STAR Format file
# Produced by PySTARRW module
#
# This is a STAR file. STAR is a superset of the CIF file type. For
# more information, please refer to International Tables for Crystallography,
# Volume G, Chapter 2.1
#
##########################################################################
data_CIF_CORE
_dictionary.title CIF_CORE
_dictionary.class Instance
_dictionary.version 3.0.04
_dictionary.date 2015-02-18
_dictionary.uri www.iucr.org/cif/dic/cif_core.dic
_dictionary.ddl_conformance 3.11.04
_dictionary.namespace CifCore
_description.text
;
The CIF_CORE dictionary records all the CORE data items defined
and used with in the Crystallographic Information Framework (CIF).
;
save_CIF_CORE
_definition.id CIF_CORE
_definition.scope Category
_definition.class Head
_definition.update 2014-06-18
_description.text
;
The CIF_CORE group contains the definitions of data items that
are common to all domains of crystallographic studies.
;
_name.category_id CIF_DIC
_name.object_id CIF_CORE
save_
save_DIFFRACTION
_definition.id DIFFRACTION
_definition.scope Category
_definition.class Set
_definition.update 2012-11-26
_description.text
;
The DICTIONARY group encompassing the CORE DIFFRACTION data items defined
and used with in the Crystallographic Information Framework (CIF).
;
_name.category_id CIF_CORE
_name.object_id DIFFRACTION
save_
save_DIFFRN
_definition.id DIFFRN
_definition.scope Category
_definition.class Set
_definition.update 2012-12-13
_description.text
;
The CATEGORY of data items used to describe the diffraction experiment.
;
_name.category_id DIFFRACTION
_name.object_id DIFFRN
save_
save__diffrn.ambient_environment
_definition.id '_diffrn.ambient_environment'
loop_
_alias.definition_id
'_diffrn.ambient_environment'
'_diffrn_ambient_environment'
_definition.update 2012-11-26
_description.text
;
The gas or liquid environment of the crystal sample, if not air.
;
_name.category_id diffrn
_name.object_id ambient_environment
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
He
vacuum
'mother liquor'
save_
save__diffrn.ambient_pressure
_definition.id '_diffrn.ambient_pressure'
loop_
_alias.definition_id
'_diffrn.ambient_pressure'
'_diffrn_ambient_pressure'
_definition.update 2012-11-26
_description.text
;
Mean hydrostatic pressure at which intensities were measured.
;
_name.category_id diffrn
_name.object_id ambient_pressure
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kilopascals
save_
save__diffrn.ambient_pressure_gt
_definition.id '_diffrn.ambient_pressure_gt'
loop_
_alias.definition_id
'_diffrn.ambient_pressure_gt'
'_diffrn_ambient_pressure_gt'
_definition.update 2012-12-13
_description.text
;
Mean hydrostatic pressure above which intensities were measured.
These items allow for a pressure range to be given.
_diffrn.ambient_pressure should be used in preference to this
item when possible.
;
_name.category_id diffrn
_name.object_id ambient_pressure_gt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kilopascals
save_
save__diffrn.ambient_pressure_lt
_definition.id '_diffrn.ambient_pressure_lt'
loop_
_alias.definition_id
'_diffrn.ambient_pressure_lt'
'_diffrn_ambient_pressure_lt'
_definition.update 2012-12-13
_description.text
;
Mean hydrostatic pressure below which intensities were measured.
These items allow for a pressure range to be given.
_diffrn.ambient_pressure should be used in preference to this
item when possible.
;
_name.category_id diffrn
_name.object_id ambient_pressure_lt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kilopascals
save_
save__diffrn.ambient_pressure_su
_definition.id '_diffrn.ambient_pressure_su'
loop_
_alias.definition_id
'_diffrn.ambient_pressure_su'
'_diffrn_ambient_pressure_su'
'_diffrn.ambient_pressure_esd'
_definition.update 2012-11-26
_description.text
;
Standard Uncertainty of the
Mean hydrostatic pressure at which intensities were measured.
;
_name.category_id diffrn
_name.object_id ambient_pressure_su
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kilopascals
save_
save__diffrn.ambient_temperature
_definition.id '_diffrn.ambient_temperature'
loop_
_alias.definition_id
'_diffrn.ambient_temperature'
'_diffrn_ambient_temperature'
'_diffrn_ambient_temp'
'_diffrn.ambient_temp'
_definition.update 2012-11-26
_description.text
;
Mean temperature at which intensities were measured.
;
_name.category_id diffrn
_name.object_id ambient_temperature
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__diffrn.ambient_temperature_details
_definition.id '_diffrn.ambient_temperature_details'
loop_
_alias.definition_id
'_diffrn.ambient_temperature_details'
'_diffrn_ambient_temp_details'
'_diffrn.ambient_temp_details'
_definition.update 2014-06-12
_description.text
;
A description of special aspects of temperature control during
data collection.
;
_name.category_id diffrn
_name.object_id ambient_temperature_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents text
save_
save__diffrn.ambient_temperature_gt
_definition.id '_diffrn.ambient_temperature_gt'
loop_
_alias.definition_id
'_diffrn.ambient_temperature_gt'
'_diffrn_ambient_temp_gt'
'_diffrn_ambient_temperature_gt'
'_diffrn.ambient_temp_gt'
_definition.update 2012-12-13
_description.text
;
Mean temperature above which intensities were measured.
These items allow for a temperature range to be given.
_diffrn.ambient_temperature should be used in preference to
this item when possible.
;
_name.category_id diffrn
_name.object_id ambient_temperature_gt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__diffrn.ambient_temperature_lt
_definition.id '_diffrn.ambient_temperature_lt'
loop_
_alias.definition_id
'_diffrn.ambient_temperature_lt'
'_diffrn_ambient_temp_lt'
'_diffrn_ambient_temperature_lt'
'_diffrn.ambient_temp_lt'
_definition.update 2012-12-13
_description.text
;
Mean temperature below which intensities were measured.
These items allow for a temperature range to be given.
_diffrn.ambient_temperature should be used in preference to
this item when possible.
;
_name.category_id diffrn
_name.object_id ambient_temperature_lt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__diffrn.ambient_temperature_su
_definition.id '_diffrn.ambient_temperature_su'
loop_
_alias.definition_id
'_diffrn.ambient_temperature_su'
'_diffrn_ambient_temperature_su'
'_diffrn_ambient_temp_su'
'_diffrn.ambient_temp_esd'
_definition.update 2012-11-26
_description.text
;
Standard Uncertainty of the
mean temperature at which intensities were measured.
;
_name.category_id diffrn
_name.object_id ambient_temperature_su
_name.linked_item_id '_diffrn.ambient_temperature'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__diffrn.crystal_id
_definition.id '_diffrn.crystal_id'
loop_
_alias.definition_id
'_diffrn.crystal_id'
'_diffrn_crystal_id'
_definition.update 2014-06-12
_description.text
;
This data item is a pointer to _exptl_crystal.id in the
EXPTL_CRYSTAL category.
;
_name.category_id diffrn
_name.object_id crystal_id
_name.linked_item_id '_exptl_crystal.id'
_type.purpose Link
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__diffrn.crystal_support
_definition.id '_diffrn.crystal_support'
loop_
_alias.definition_id
'_diffrn.crystal_support'
_definition.update 2014-06-12
_description.text
;
The physical device used to support the crystal during data
collection.
;
_name.category_id diffrn
_name.object_id crystal_support
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'glass capillary'
'quartz capillary'
fiber
'metal loop'
save_
save__diffrn.crystal_treatment
_definition.id '_diffrn.crystal_treatment'
loop_
_alias.definition_id
'_diffrn.crystal_treatment'
'_diffrn_crystal_treatment'
_definition.update 2012-11-26
_description.text
;
Remarks about how the crystal was treated prior to intensity measurement.
Particularly relevant when intensities were measured at low temperature.
;
_name.category_id diffrn
_name.object_id crystal_treatment
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'equilibrated in hutch for 24 hours'
'flash frozen in liquid nitrogen'
'slow cooled with direct air stream'
save_
save__diffrn.measured_fraction_theta_full
_definition.id '_diffrn.measured_fraction_theta_full'
loop_
_alias.definition_id
'_diffrn.measured_fraction_theta_full'
'_diffrn_measured_fraction_theta_full'
_definition.update 2013-01-20
_description.text
;
Fraction of unique (symmetry-independent) reflections measured
out to _diffrn_reflns.theta_full.
;
_name.category_id diffrn
_name.object_id measured_fraction_theta_full
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save__diffrn.measured_fraction_theta_max
_definition.id '_diffrn.measured_fraction_theta_max'
loop_
_alias.definition_id
'_diffrn.measured_fraction_theta_max'
'_diffrn_measured_fraction_theta_max'
_definition.update 2013-01-20
_description.text
;
Fraction of unique (symmetry-independent) reflections measured
out to _diffrn_reflns.theta_max.
;
_name.category_id diffrn
_name.object_id measured_fraction_theta_max
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save__diffrn.special_details
_definition.id '_diffrn.special_details'
loop_
_alias.definition_id
'_diffrn.special_details'
'_diffrn_special_details'
'_diffrn.details'
_definition.update 2012-11-26
_description.text
;
Special details of the diffraction measurement process. Should include
information about source instability, crystal motion, degradation, etc.
;
_name.category_id diffrn
_name.object_id special_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
;
The results may not be entirely reliable as the measurement was
made during a heat wave when the air-conditioning had failed.
;
save_
save__diffrn.symmetry_description
_definition.id '_diffrn.symmetry_description'
loop_
_alias.definition_id
'_diffrn.symmetry_description'
'_diffrn_symmetry_description'
_definition.update 2012-11-26
_description.text
;
Recorded diffraction point symmetry, systematic absences and possible
space group(s) or superspace group(s) compatible with these.
;
_name.category_id diffrn
_name.object_id symmetry_description
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_DIFFRN_ATTENUATOR
_definition.id DIFFRN_ATTENUATOR
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items which specify the attenuators used in the
diffraction source.
;
_name.category_id DIFFRN
_name.object_id DIFFRN_ATTENUATOR
_category.key_id '_diffrn_attenuator.key'
_category.key_list ['_diffrn_attenuator.code']
save_
save__diffrn_attenuator.code
_definition.id '_diffrn_attenuator.code'
loop_
_alias.definition_id
'_diffrn_attenuator.code'
'_diffrn_attenuator_code'
_definition.update 2012-11-26
_description.text
;
Code identifying a particular attenuator setting; referenced by the
_diffrn_refln.attenuator_code which is stored with the intensities.
;
_name.category_id diffrn_attenuator
_name.object_id code
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__diffrn_attenuator.key
_definition.id '_diffrn_attenuator.key'
loop_
_alias.definition_id
'_diffrn_attenuator.key'
_definition.update 2012-11-26
_description.text
;
Value is a unique key to a set of DIFFRN_ATTENUATOR items
in a looped list.
;
_name.category_id diffrn_attenuator
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _diffrn_attenuator.key = _diffrn_attenuator.code'
save_
save__diffrn_attenuator.material
_definition.id '_diffrn_attenuator.material'
loop_
_alias.definition_id
'_diffrn_attenuator.material'
'_diffrn_attenuator_material'
_definition.update 2012-11-26
_description.text
;
Description of the material from which the attenuator is made.
;
_name.category_id diffrn_attenuator
_name.object_id material
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__diffrn_attenuator.scale
_definition.id '_diffrn_attenuator.scale'
loop_
_alias.definition_id
'_diffrn_attenuator.scale'
'_diffrn_attenuator_scale'
_definition.update 2012-11-26
_description.text
;
The scale factor applied to a measured intensity if it is reduced by
an attenuator identified by _diffrn_attenuator.code.
;
_name.category_id diffrn_attenuator
_name.object_id scale
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 1.0:
_units.code none
save_
save_DIFFRN_DETECTOR
_definition.id DIFFRN_DETECTOR
_definition.scope Category
_definition.class Set
_definition.update 2012-11-26
_description.text
;
The CATEGORY of data items which specify the detectors used in the
in the measurement of diffraction intensities.
;
_name.category_id DIFFRN
_name.object_id DIFFRN_DETECTOR
save_
save__diffrn_detector.area_resol_mean
_definition.id '_diffrn_detector.area_resol_mean'
loop_
_alias.definition_id
'_diffrn_detector.area_resol_mean'
'_diffrn_detector_area_resol_mean'
_definition.update 2012-11-26
_description.text
;
The resolution limit of an area diffraction radiation detector.
;
_name.category_id diffrn_detector
_name.object_id area_resol_mean
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code pixels_per_millimetre
save_
save__diffrn_detector.description
_definition.id '_diffrn_detector.description'
loop_
_alias.definition_id
'_diffrn_detector.description'
'_diffrn_radiation_detector'
'_diffrn_detector'
'_diffrn_detector.detector'
_definition.update 2012-11-26
_description.text
;
Description of the type of diffraction radiation detector.
;
_name.category_id diffrn_detector
_name.object_id description
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
save_
save__diffrn_detector.details
_definition.id '_diffrn_detector.details'
loop_
_alias.definition_id
'_diffrn_detector.details'
'_diffrn_detector_details'
_definition.update 2012-11-26
_description.text
;
Description of special aspects of the radiation detector.
;
_name.category_id diffrn_detector
_name.object_id details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__diffrn_detector.dtime
_definition.id '_diffrn_detector.dtime'
loop_
_alias.definition_id
'_diffrn_detector.dtime'
'_diffrn_detector_dtime'
'_diffrn_radiation.detector_dtime'
'_diffrn_radiation_detector_dtime'
_definition.update 2012-11-26
_description.text
;
The maximum time between two detector signals that cannot be resolved.
;
_name.category_id diffrn_detector
_name.object_id dtime
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code microseconds
save_
save__diffrn_detector.make
_definition.id '_diffrn_detector.make'
loop_
_alias.definition_id
'_diffrn_detector.make'
'_diffrn_detector_type'
'_diffrn_detector.type'
_definition.update 2012-11-26
_description.text
;
The make, model or name of the diffraction radiation detector.
;
_name.category_id diffrn_detector
_name.object_id make
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_DIFFRN_MEASUREMENT
_definition.id DIFFRN_MEASUREMENT
_definition.scope Category
_definition.class Set
_definition.update 2012-11-26
_description.text
;
The CATEGORY of data items which specify the details of the
diffraction measurement.
;
_name.category_id DIFFRN
_name.object_id DIFFRN_MEASUREMENT
save_
save__diffrn_measurement.details
_definition.id '_diffrn_measurement.details'
loop_
_alias.definition_id
'_diffrn_measurement.details'
'_diffrn_measurement_details'
'_diffrn.measurement_details'
_definition.update 2012-11-26
_description.text
;
Description of special aspects of the diffraction measurement.
;
_name.category_id diffrn_measurement
_name.object_id details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'440 frames of 0.25\%'
save_
save__diffrn_measurement.device_class
_definition.id '_diffrn_measurement.device_class'
loop_
_alias.definition_id
'_diffrn_measurement.device_class'
'_diffrn_measurement_device'
'_diffrn.measurement_device_class'
'_diffrn_measurement.device'
_definition.update 2012-11-26
_description.text
;
Type of goniometer device used to mount and orient the specimen.
;
_name.category_id diffrn_measurement
_name.object_id device_class
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'three-circle diffractometer'
'four-circle diffractometer'
'\k-geometry diffractometer'
'oscillation camera'
'precession camera'
save_
save__diffrn_measurement.device_details
_definition.id '_diffrn_measurement.device_details'
loop_
_alias.definition_id
'_diffrn_measurement.device_details'
'_diffrn_measurement_device_details'
'_diffrn.measurement_device_details'
_definition.update 2012-11-26
_description.text
;
Details of the goniometer device used in the diffraction experiment.
;
_name.category_id diffrn_measurement
_name.object_id device_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'commercial goniometer modified locally to allow for 90\% \t arc'
save_
save__diffrn_measurement.device_make
_definition.id '_diffrn_measurement.device_make'
loop_
_alias.definition_id
'_diffrn_measurement.device_make'
'_diffrn_measurement_device_type'
'_diffrn.measurement_device_make'
'_diffrn_measurement.device_type'
_definition.update 2013-03-07
_description.text
;
The make, model or name of the goniometer device used.
;
_name.category_id diffrn_measurement
_name.object_id device_make
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'Supper model q'
'Huber model r'
'Enraf-Nonius model s'
home-made
save_
save__diffrn_measurement.method
_definition.id '_diffrn_measurement.method'
loop_
_alias.definition_id
'_diffrn_measurement.method'
'_diffrn_measurement_method'
'_diffrn.measurement_method'
_definition.update 2012-11-26
_description.text
;
Description of scan method used to measure diffraction intensities.
;
_name.category_id diffrn_measurement
_name.object_id method
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'profile data from \q/2\q scans'
save_
save__diffrn_measurement.specimen_support
_definition.id '_diffrn_measurement.specimen_support'
loop_
_alias.definition_id
'_diffrn_measurement.specimen_support'
'_diffrn_measurement_specimen_support'
'_diffrn.measurement_specimen_support'
_definition.update 2013-01-23
_description.text
;
Mounting method for the crystal specimum during data collection.
;
_name.category_id diffrn_measurement
_name.object_id specimen_support
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'glass capillary'
'quartz capillary'
fiber
'metal loop'
save_
save_DIFFRN_ORIENT
_definition.id DIFFRN_ORIENT
_definition.scope Category
_definition.class Set
_definition.update 2012-11-26
_description.text
;
The CATEGORY of data items which specify the orientation of the crystal
axes to the diffractometer goniometer.
;
_name.category_id DIFFRN
_name.object_id DIFFRN_ORIENT
save_
save_DIFFRN_ORIENT_MATRIX
_definition.id DIFFRN_ORIENT_MATRIX
_definition.scope Category
_definition.class Set
_definition.update 2012-11-26
_description.text
;
The CATEGORY of data items which specify the matrix specifying the
orientation of the crystal axes to the diffractometer goniometer.
;
_name.category_id DIFFRN_ORIENT
_name.object_id DIFFRN_ORIENT_MATRIX
save_
save__diffrn_orient_matrix.type
_definition.id '_diffrn_orient_matrix.type'
loop_
_alias.definition_id
'_diffrn_orient_matrix.type'
'_diffrn_orient_matrix_type'
_definition.update 2012-11-26
_description.text
;
Description of orientation matrix and how it should be applied to define
the orientation of the crystal with respect to the diffractometer axes.
;
_name.category_id diffrn_orient_matrix
_name.object_id type
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__diffrn_orient_matrix.UB_11
_definition.id '_diffrn_orient_matrix.UB_11'
loop_
_alias.definition_id
'_diffrn_orient_matrix.UB_11'
'_diffrn_orient_matrix_UB_11'
'_diffrn_orient_matrix.UB[1][1]'
_name.category_id diffrn_orient_matrix
_name.object_id UB_11
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix of
the orientation of the crystal axes to the diffractometer goniometer.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_orient_matrix.UB_12
_definition.id '_diffrn_orient_matrix.UB_12'
loop_
_alias.definition_id
'_diffrn_orient_matrix.UB_12'
'_diffrn_orient_matrix_UB_12'
'_diffrn_orient_matrix.UB[1][2]'
_name.category_id diffrn_orient_matrix
_name.object_id UB_12
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix of
the orientation of the crystal axes to the diffractometer goniometer.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_orient_matrix.UB_13
_definition.id '_diffrn_orient_matrix.UB_13'
loop_
_alias.definition_id
'_diffrn_orient_matrix.UB_13'
'_diffrn_orient_matrix_UB_13'
'_diffrn_orient_matrix.UB[1][3]'
_name.category_id diffrn_orient_matrix
_name.object_id UB_13
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix of
the orientation of the crystal axes to the diffractometer goniometer.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_orient_matrix.UB_21
_definition.id '_diffrn_orient_matrix.UB_21'
loop_
_alias.definition_id
'_diffrn_orient_matrix.UB_21'
'_diffrn_orient_matrix_UB_21'
'_diffrn_orient_matrix.UB[2][1]'
_name.category_id diffrn_orient_matrix
_name.object_id UB_21
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix of
the orientation of the crystal axes to the diffractometer goniometer.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_orient_matrix.UB_22
_definition.id '_diffrn_orient_matrix.UB_22'
loop_
_alias.definition_id
'_diffrn_orient_matrix.UB_22'
'_diffrn_orient_matrix_UB_22'
'_diffrn_orient_matrix.UB[2][2]'
_name.category_id diffrn_orient_matrix
_name.object_id UB_22
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix of
the orientation of the crystal axes to the diffractometer goniometer.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_orient_matrix.UB_23
_definition.id '_diffrn_orient_matrix.UB_23'
loop_
_alias.definition_id
'_diffrn_orient_matrix.UB_23'
'_diffrn_orient_matrix_UB_23'
'_diffrn_orient_matrix.UB[2][3]'
_name.category_id diffrn_orient_matrix
_name.object_id UB_23
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix of
the orientation of the crystal axes to the diffractometer goniometer.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_orient_matrix.UB_31
_definition.id '_diffrn_orient_matrix.UB_31'
loop_
_alias.definition_id
'_diffrn_orient_matrix.UB_31'
'_diffrn_orient_matrix_UB_31'
'_diffrn_orient_matrix.UB[3][1]'
_name.category_id diffrn_orient_matrix
_name.object_id UB_31
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix of
the orientation of the crystal axes to the diffractometer goniometer.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_orient_matrix.UB_32
_definition.id '_diffrn_orient_matrix.UB_32'
loop_
_alias.definition_id
'_diffrn_orient_matrix.UB_32'
'_diffrn_orient_matrix_UB_32'
'_diffrn_orient_matrix.UB[3][2]'
_name.category_id diffrn_orient_matrix
_name.object_id UB_32
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix of
the orientation of the crystal axes to the diffractometer goniometer.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_orient_matrix.UB_33
_definition.id '_diffrn_orient_matrix.UB_33'
loop_
_alias.definition_id
'_diffrn_orient_matrix.UB_33'
'_diffrn_orient_matrix_UB_33'
'_diffrn_orient_matrix.UB[3][3]'
_name.category_id diffrn_orient_matrix
_name.object_id UB_33
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix of
the orientation of the crystal axes to the diffractometer goniometer.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_orient_matrix.UBIJ
_definition.id '_diffrn_orient_matrix.UBIJ'
loop_
_alias.definition_id
'_diffrn_orient_matrix.UBIJ'
_definition.update 2012-11-26
_description.text
;
The 3x3 matrix specifying the orientation of the crystal with
respect to the diffractometer axes.
;
_name.category_id diffrn_orient_matrix
_name.object_id UBIJ
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3 3]
loop_
_method.purpose
_method.expression
Evaluation
;
With o as diffrn_orient_matrix
_diffrn_orient_matrix.UBIJ = [[ o.ub_11, o.ub_12, o.ub_13 ],
[ o.ub_21, o.ub_22, o.ub_23 ],
[ o.ub_31, o.ub_32, o.ub_33 ]]
;
save_
save_DIFFRN_ORIENT_REFLN
_definition.id DIFFRN_ORIENT_REFLN
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items which specify the reflections used to
calculate the matrix which gives the orientation of the crystal
axes to the diffractometer goniometer.
;
_name.category_id DIFFRN_ORIENT
_name.object_id DIFFRN_ORIENT_REFLN
_category.key_id '_diffrn_orient_refln.key'
_category.key_list ['_diffrn_orient_refln.index_h'
'_diffrn_orient_refln.index_k'
'_diffrn_orient_refln.index_l']
save_
save__diffrn_orient_refln.angle_chi
_definition.id '_diffrn_orient_refln.angle_chi'
loop_
_alias.definition_id
'_diffrn_orient_refln.angle_chi'
'_diffrn_orient_refln_angle_chi'
_name.category_id diffrn_orient_refln
_name.object_id angle_chi
_type.contents Real
_type.purpose Measurand
_description.text
;
Diffractometer angle of a reflection measured at the centre of the
diffraction peak and used to determine _diffrn_orient_matrix.UBIJ.
;
_enumeration.range -180.:180.
_type.source Recorded
_type.container Single
_definition.update 2013-04-15
_units.code degrees
save_
save__diffrn_orient_refln.angle_kappa
_definition.id '_diffrn_orient_refln.angle_kappa'
loop_
_alias.definition_id
'_diffrn_orient_refln.angle_kappa'
'_diffrn_orient_refln_angle_kappa'
_name.category_id diffrn_orient_refln
_name.object_id angle_kappa
_type.contents Real
_type.purpose Measurand
_description.text
;
Diffractometer angle of a reflection measured at the centre of the
diffraction peak and used to determine _diffrn_orient_matrix.UBIJ.
;
_enumeration.range -180.:180.
_type.source Recorded
_type.container Single
_definition.update 2013-04-15
_units.code degrees
save_
save__diffrn_orient_refln.angle_omega
_definition.id '_diffrn_orient_refln.angle_omega'
loop_
_alias.definition_id
'_diffrn_orient_refln.angle_omega'
'_diffrn_orient_refln_angle_omega'
_name.category_id diffrn_orient_refln
_name.object_id angle_omega
_type.contents Real
_type.purpose Measurand
_description.text
;
Diffractometer angle of a reflection measured at the centre of the
diffraction peak and used to determine _diffrn_orient_matrix.UBIJ.
;
_enumeration.range -180.:180.
_type.source Recorded
_type.container Single
_definition.update 2013-04-15
_units.code degrees
save_
save__diffrn_orient_refln.angle_phi
_definition.id '_diffrn_orient_refln.angle_phi'
loop_
_alias.definition_id
'_diffrn_orient_refln.angle_phi'
'_diffrn_orient_refln_angle_phi'
_name.category_id diffrn_orient_refln
_name.object_id angle_phi
_type.contents Real
_type.purpose Measurand
_description.text
;
Diffractometer angle of a reflection measured at the centre of the
diffraction peak and used to determine _diffrn_orient_matrix.UBIJ.
;
_enumeration.range -180.:180.
_type.source Recorded
_type.container Single
_definition.update 2013-04-15
_units.code degrees
save_
save__diffrn_orient_refln.angle_psi
_definition.id '_diffrn_orient_refln.angle_psi'
loop_
_alias.definition_id
'_diffrn_orient_refln.angle_psi'
'_diffrn_orient_refln_angle_psi'
_name.category_id diffrn_orient_refln
_name.object_id angle_psi
_type.contents Real
_type.purpose Measurand
_description.text
;
Diffractometer angle of a reflection measured at the centre of the
diffraction peak and used to determine _diffrn_orient_matrix.UBIJ.
;
_enumeration.range -180.:180.
_type.source Recorded
_type.container Single
_definition.update 2013-04-15
_units.code degrees
save_
save__diffrn_orient_refln.angle_theta
_definition.id '_diffrn_orient_refln.angle_theta'
loop_
_alias.definition_id
'_diffrn_orient_refln.angle_theta'
'_diffrn_orient_refln_angle_theta'
_name.category_id diffrn_orient_refln
_name.object_id angle_theta
_type.contents Real
_type.purpose Measurand
_description.text
;
Diffractometer angle of a reflection measured at the centre of the
diffraction peak and used to determine _diffrn_orient_matrix.UBIJ.
;
_enumeration.range -180.:180.
_type.source Recorded
_type.container Single
_definition.update 2013-04-15
_units.code degrees
save_
save__diffrn_orient_refln.hkl
_definition.id '_diffrn_orient_refln.hkl'
loop_
_alias.definition_id
'_diffrn_orient_refln.hkl'
_definition.update 2012-11-26
_description.text
;
Miller indices of a reflection used to define the orientation matrix.
;
_name.category_id diffrn_orient_refln
_name.object_id hkl
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Integer
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With a as diffrn_orient_refln
_diffrn_orient_refln.hkl = [a.index_h, a.index_k, a.index_l]
;
save_
save__diffrn_orient_refln.index_h
_definition.id '_diffrn_orient_refln.index_h'
loop_
_alias.definition_id
'_diffrn_orient_refln.index_h'
'_diffrn_orient_refln_index_h'
_name.category_id diffrn_orient_refln
_name.object_id index_h
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__diffrn_orient_refln.index_k
_definition.id '_diffrn_orient_refln.index_k'
loop_
_alias.definition_id
'_diffrn_orient_refln.index_k'
'_diffrn_orient_refln_index_k'
_name.category_id diffrn_orient_refln
_name.object_id index_k
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__diffrn_orient_refln.index_l
_definition.id '_diffrn_orient_refln.index_l'
loop_
_alias.definition_id
'_diffrn_orient_refln.index_l'
'_diffrn_orient_refln_index_l'
_name.category_id diffrn_orient_refln
_name.object_id index_l
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__diffrn_orient_refln.key
_definition.id '_diffrn_orient_refln.key'
loop_
_alias.definition_id
'_diffrn_orient_refln.key'
_definition.update 2012-11-26
_description.text
;
Value is a unique key to a set of DIFFRN_ORIENT_REFLN items
in a looped list.
;
_name.category_id diffrn_orient_refln
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Matrix
_type.contents Integer
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation ' _diffrn_orient_refln.key = _diffrn_orient_refln.hkl'
save_
save_DIFFRN_RADIATION
_definition.id DIFFRN_RADIATION
_definition.scope Category
_definition.class Set
_definition.update 2012-11-26
_description.text
;
The CATEGORY of data items which specify the wavelength of the
radiation used in measuring diffraction intensities. Items may be
looped to identify and assign weights to distinct wavelength
components from a polychromatic beam.
;
_name.category_id DIFFRN
_name.object_id DIFFRN_RADIATION
save_
save__diffrn_radiation.collimation
_definition.id '_diffrn_radiation.collimation'
loop_
_alias.definition_id
'_diffrn_radiation.collimation'
'_diffrn_radiation_collimation'
_definition.update 2012-11-26
_description.text
;
Description of the collimation or focusing applied to the radiation.
;
_name.category_id diffrn_radiation
_name.object_id collimation
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'0.3 mm double-pinhole'
'0.5 mm'
'focusing mirrors'
save_
save__diffrn_radiation.filter_edge
_definition.id '_diffrn_radiation.filter_edge'
loop_
_alias.definition_id
'_diffrn_radiation.filter_edge'
'_diffrn_radiation_filter_edge'
_definition.update 2012-11-26
_description.text
;
Absorption edge of the radiation filter used.
;
_name.category_id diffrn_radiation
_name.object_id filter_edge
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__diffrn_radiation.inhomogeneity
_definition.id '_diffrn_radiation.inhomogeneity'
loop_
_alias.definition_id
'_diffrn_radiation.inhomogeneity'
'_diffrn_radiation_inhomogeneity'
_definition.update 2012-11-26
_description.text
;
Half-width of the incident beam perpendicular to the diffraction plane.
;
_name.category_id diffrn_radiation
_name.object_id inhomogeneity
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code millimetres
save_
save__diffrn_radiation.monochromator
_definition.id '_diffrn_radiation.monochromator'
loop_
_alias.definition_id
'_diffrn_radiation.monochromator'
'_diffrn_radiation_monochromator'
_definition.update 2012-11-26
_description.text
;
Description of the method used to obtain monochromatic radiation.
If a monochromator crystal is used the material and the indices of
the Bragg reflection are specified.
;
_name.category_id diffrn_radiation
_name.object_id monochromator
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'Zr filter'
'Ge 220'
none
'equatorial mounted graphite'
save_
save__diffrn_radiation.polarisn_norm
_definition.id '_diffrn_radiation.polarisn_norm'
loop_
_alias.definition_id
'_diffrn_radiation.polarisn_norm'
'_diffrn_radiation_polarisn_norm'
_definition.update 2012-11-26
_description.text
;
The angle, as viewed from the specimen, between the perpendicular
component of the polarisation and the diffraction plane.
;
_name.category_id diffrn_radiation
_name.object_id polarisn_norm
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range -180.0:180.0
_units.code degrees
save_
save__diffrn_radiation.polarisn_ratio
_definition.id '_diffrn_radiation.polarisn_ratio'
loop_
_alias.definition_id
'_diffrn_radiation.polarisn_ratio'
'_diffrn_radiation_polarisn_ratio'
_definition.update 2012-11-26
_description.text
;
Polarisation ratio of the diffraction beam incident on the crystal.
It is the ratio of the perpendicularly polarised to the parallel
polarised component of the radiation. The perpendicular component
forms an angle of _diffrn_radiation.polarisn_norm to the normal to
the diffraction plane of the sample (i.e. the plane containing the
incident and reflected beams).
;
_name.category_id diffrn_radiation
_name.object_id polarisn_ratio
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__diffrn_radiation.probe
_definition.id '_diffrn_radiation.probe'
loop_
_alias.definition_id
'_diffrn_radiation.probe'
'_diffrn_radiation_probe'
_definition.update 2012-11-26
_description.text
;
Enumerated code for the nature of radiation used (i.e. name of
subatomic particle or region of the electromagnetic spectrum).
;
_name.category_id diffrn_radiation
_name.object_id probe
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
x-ray
neutron
electron
gamma
_enumeration.default x-ray
save_
save__diffrn_radiation.type
_definition.id '_diffrn_radiation.type'
loop_
_alias.definition_id
'_diffrn_radiation.type'
'_diffrn_radiation_type'
_definition.update 2013-03-23
_description.text
;
Details of the radiation source or energy spectrum.
;
_name.category_id diffrn_radiation
_name.object_id type
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'Mo K\a'
'Cu K\a'
'Cu K\a~1~'
'Cu K-L~2,3~'
white-beam
save_
save__diffrn_radiation.xray_symbol
_definition.id '_diffrn_radiation.xray_symbol'
loop_
_alias.definition_id
'_diffrn_radiation.xray_symbol'
'_diffrn_radiation_xray_symbol'
_definition.update 2012-11-26
_description.text
;
IUPAC symbol for the X-ray wavelength for probe radiation.
;
_name.category_id diffrn_radiation
_name.object_id xray_symbol
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
K-L~3~ 'K\a~1~ in older Siegbahn notation'
K-L~2~ 'K\a~2~ in older Siegbahn notation'
K-M~3~ 'K\b~1~ in older Siegbahn notation'
'K-L~2,3~' 'use where K-L~3~ and K-L~2~ are not resolved'
_enumeration.default K-L~3~
save_
save_DIFFRN_RADIATION_WAVELENGTH
_definition.id DIFFRN_RADIATION_WAVELENGTH
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items which specify the wavelength of the
radiation used in measuring diffraction intensities. Items may be
looped to identify and assign weights to distinct wavelength
components from a polychromatic beam.
;
_name.category_id DIFFRN_RADIATION
_name.object_id DIFFRN_RADIATION_WAVELENGTH
_category.key_id '_diffrn_radiation_wavelength.key'
_category.key_list ['_diffrn_radiation_wavelength.id']
save_
save__diffrn_radiation_wavelength.details
_definition.id '_diffrn_radiation_wavelength.details'
loop_
_alias.definition_id
'_diffrn_radiation_wavelength.details'
'_diffrn_radiation_wavelength_details'
'_diffrn_radiation.wavelength_details'
_definition.update 2012-11-26
_description.text
;
Information about the determination of the radiation
diffrn_radiation_wavelength that is not conveyed completely by an
enumerated value of _diffrn_radiation_wavelength.determination.
;
_name.category_id diffrn_radiation_wavelength
_name.object_id details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__diffrn_radiation_wavelength.determination
_definition.id '_diffrn_radiation_wavelength.determination'
loop_
_alias.definition_id
'_diffrn_radiation_wavelength.determination'
'_diffrn_radiation_wavelength_determination'
'_diffrn_radiation.wavelength_determination'
_definition.update 2012-11-26
_description.text
;
Information about the determination of the radiation
wavelength that is not conveyed completely by an
enumerated value of _diffrn_radiation_wavelength.determination.
;
_name.category_id diffrn_radiation_wavelength
_name.object_id determination
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
fundamental 'Fundamental property of matter e.g. MoK\alpha'
estimated 'Estimated e.g. from monochromator angle or time of flight'
refined 'Refined using a standard crystal with known cell parameters'
_enumeration.default fundamental
save_
save__diffrn_radiation_wavelength.id
_definition.id '_diffrn_radiation_wavelength.id'
loop_
_alias.definition_id
'_diffrn_radiation_wavelength.id'
'_diffrn_radiation_wavelength_id'
'_diffrn_radiation.wavelength_id'
_definition.update 2012-11-26
_description.text
;
Code identifying a radiation used in the diffraction measurements.
This is linked to _diffrn_refln.wavelength_id and _refln.wavelength_id
;
_name.category_id diffrn_radiation_wavelength
_name.object_id id
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_description_example.case
x2
save_
save__diffrn_radiation_wavelength.key
_definition.id '_diffrn_radiation_wavelength.key'
loop_
_alias.definition_id
'_diffrn_radiation_wavelength.key'
_definition.update 2012-11-26
_description.text
;
Value is a unique key to a set of DIFFRN_RADIATION_WAVELENGTH items
in a looped list.
;
_name.category_id diffrn_radiation_wavelength
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _diffrn_radiation_wavelength.key = _diffrn_radiation_wavelength.id'
save_
save__diffrn_radiation_wavelength.value
_definition.id '_diffrn_radiation_wavelength.value'
loop_
_alias.definition_id
'_diffrn_radiation_wavelength.value'
'_diffrn_radiation_wavelength'
'_diffrn_radiation_wavelength.wavelength'
_definition.update 2012-11-26
_description.text
;
Wavelength of radiation used in diffraction measurements.
;
_name.category_id diffrn_radiation_wavelength
_name.object_id value
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__diffrn_radiation_wavelength.wt
_definition.id '_diffrn_radiation_wavelength.wt'
loop_
_alias.definition_id
'_diffrn_radiation_wavelength.wt'
'_diffrn_radiation_wavelength_wt'
_definition.update 2012-11-26
_description.text
;
Relative intensity of a radiation used in the diffraction measurements.
;
_name.category_id diffrn_radiation_wavelength
_name.object_id wt
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_enumeration.default 1.0
_units.code none
save_
save_DIFFRN_REFLN
_definition.id DIFFRN_REFLN
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items which specify the reflection measurements,
prior to data reduction and merging.
;
_name.category_id DIFFRN
_name.object_id DIFFRN_REFLN
_category.key_id '_diffrn_refln.key'
_category.key_list ['_diffrn_refln.index_h' '_diffrn_refln.index_k'
'_diffrn_refln.index_l']
save_
save__diffrn_refln.angle_chi
_definition.id '_diffrn_refln.angle_chi'
loop_
_alias.definition_id
'_diffrn_refln.angle_chi'
'_diffrn_refln_angle_chi'
_name.category_id diffrn_refln
_name.object_id angle_chi
_type.contents Real
_type.purpose Number
_description.text
;
Diffractometer angle at which the intensity is measured. This was
calculated from the specified orientation matrix and the original
measured cell dimensions before any subsequent transformations.
;
_enumeration.range -180.:180.
_type.source Derived
_type.container Single
_definition.update 2013-04-15
_units.code degrees
save_
save__diffrn_refln.angle_kappa
_definition.id '_diffrn_refln.angle_kappa'
loop_
_alias.definition_id
'_diffrn_refln.angle_kappa'
'_diffrn_refln_angle_kappa'
_name.category_id diffrn_refln
_name.object_id angle_kappa
_type.contents Real
_type.purpose Number
_description.text
;
Diffractometer angle at which the intensity is measured. This was
calculated from the specified orientation matrix and the original
measured cell dimensions before any subsequent transformations.
;
_enumeration.range -180.:180.
_type.source Derived
_type.container Single
_definition.update 2013-04-15
_units.code degrees
save_
save__diffrn_refln.angle_omega
_definition.id '_diffrn_refln.angle_omega'
loop_
_alias.definition_id
'_diffrn_refln.angle_omega'
'_diffrn_refln_angle_omega'
_name.category_id diffrn_refln
_name.object_id angle_omega
_type.contents Real
_type.purpose Number
_description.text
;
Diffractometer angle at which the intensity is measured. This was
calculated from the specified orientation matrix and the original
measured cell dimensions before any subsequent transformations.
;
_enumeration.range -180.:180.
_type.source Derived
_type.container Single
_definition.update 2013-04-15
_units.code degrees
save_
save__diffrn_refln.angle_phi
_definition.id '_diffrn_refln.angle_phi'
loop_
_alias.definition_id
'_diffrn_refln.angle_phi'
'_diffrn_refln_angle_phi'
_name.category_id diffrn_refln
_name.object_id angle_phi
_type.contents Real
_type.purpose Number
_description.text
;
Diffractometer angle at which the intensity is measured. This was
calculated from the specified orientation matrix and the original
measured cell dimensions before any subsequent transformations.
;
_enumeration.range -180.:180.
_type.source Derived
_type.container Single
_definition.update 2013-04-15
_units.code degrees
save_
save__diffrn_refln.angle_psi
_definition.id '_diffrn_refln.angle_psi'
loop_
_alias.definition_id
'_diffrn_refln.angle_psi'
'_diffrn_refln_angle_psi'
_name.category_id diffrn_refln
_name.object_id angle_psi
_type.contents Real
_type.purpose Number
_description.text
;
Diffractometer angle at which the intensity is measured. This was
calculated from the specified orientation matrix and the original
measured cell dimensions before any subsequent transformations.
;
_enumeration.range -180.:180.
_type.source Derived
_type.container Single
_definition.update 2013-04-15
_units.code degrees
save_
save__diffrn_refln.angle_theta
_definition.id '_diffrn_refln.angle_theta'
loop_
_alias.definition_id
'_diffrn_refln.angle_theta'
'_diffrn_refln_angle_theta'
_name.category_id diffrn_refln
_name.object_id angle_theta
_type.contents Real
_type.purpose Number
_description.text
;
Diffractometer angle at which the intensity is measured. This was
calculated from the specified orientation matrix and the original
measured cell dimensions before any subsequent transformations.
;
_enumeration.range -180.:180.
_type.source Derived
_type.container Single
_definition.update 2013-04-15
_units.code degrees
save_
save__diffrn_refln.attenuator_code
_definition.id '_diffrn_refln.attenuator_code'
loop_
_alias.definition_id
'_diffrn_refln.attenuator_code'
'_diffrn_refln_attenuator_code'
_definition.update 2012-11-26
_description.text
;
Code identifying any attenuator setting for this reflection.
;
_name.category_id diffrn_refln
_name.object_id attenuator_code
_name.linked_item_id '_diffrn_attenuator.code'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save__diffrn_refln.class_code
_definition.id '_diffrn_refln.class_code'
loop_
_alias.definition_id
'_diffrn_refln.class_code'
'_diffrn_refln_class_code'
_definition.update 2012-11-26
_description.text
;
Code for reflection class, if assigned. e.g. modulated structures
;
_name.category_id diffrn_refln
_name.object_id class_code
_name.linked_item_id '_diffrn_reflns_class.code'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save__diffrn_refln.counts_bg_1
_definition.id '_diffrn_refln.counts_bg_1'
loop_
_alias.definition_id
'_diffrn_refln.counts_bg_1'
'_diffrn_refln_counts_bg_1'
_name.category_id diffrn_refln
_name.object_id counts_bg_1
_type.contents Count
_type.purpose Measurand
_description.text
;
The set of data items which specify the diffractometer counts.
Background counts before the peak, background after the peak,
net counts after background removed, counts for peak scan or position,
and the total counts (background plus peak).
;
_enumeration.range 0:
_type.source Recorded
_type.container Single
_definition.update 2012-10-16
_units.code none
save_
save__diffrn_refln.counts_bg_2
_definition.id '_diffrn_refln.counts_bg_2'
loop_
_alias.definition_id
'_diffrn_refln.counts_bg_2'
'_diffrn_refln_counts_bg_2'
_name.category_id diffrn_refln
_name.object_id counts_bg_2
_type.contents Count
_type.purpose Measurand
_description.text
;
The set of data items which specify the diffractometer counts.
Background counts before the peak, background after the peak,
net counts after background removed, counts for peak scan or position,
and the total counts (background plus peak).
;
_enumeration.range 0:
_type.source Recorded
_type.container Single
_definition.update 2012-10-16
_units.code none
save_
save__diffrn_refln.counts_net
_definition.id '_diffrn_refln.counts_net'
loop_
_alias.definition_id
'_diffrn_refln.counts_net'
'_diffrn_refln_counts_net'
_name.category_id diffrn_refln
_name.object_id counts_net
_type.contents Count
_type.purpose Measurand
_description.text
;
The set of data items which specify the diffractometer counts.
Background counts before the peak, background after the peak,
net counts after background removed, counts for peak scan or position,
and the total counts (background plus peak).
;
_enumeration.range 0:
_type.source Recorded
_type.container Single
_definition.update 2012-10-16
_units.code none
save_
save__diffrn_refln.counts_peak
_definition.id '_diffrn_refln.counts_peak'
loop_
_alias.definition_id
'_diffrn_refln.counts_peak'
'_diffrn_refln_counts_peak'
_name.category_id diffrn_refln
_name.object_id counts_peak
_type.contents Count
_type.purpose Measurand
_description.text
;
The set of data items which specify the diffractometer counts.
Background counts before the peak, background after the peak,
net counts after background removed, counts for peak scan or position,
and the total counts (background plus peak).
;
_enumeration.range 0:
_type.source Recorded
_type.container Single
_definition.update 2012-10-16
_units.code none
save_
save__diffrn_refln.counts_total
_definition.id '_diffrn_refln.counts_total'
loop_
_alias.definition_id
'_diffrn_refln.counts_total'
'_diffrn_refln_counts_total'
_name.category_id diffrn_refln
_name.object_id counts_total
_type.contents Count
_type.purpose Measurand
_description.text
;
The set of data items which specify the diffractometer counts.
Background counts before the peak, background after the peak,
net counts after background removed, counts for peak scan or position,
and the total counts (background plus peak).
;
_enumeration.range 0:
_type.source Recorded
_type.container Single
_definition.update 2012-10-16
_units.code none
save_
save__diffrn_refln.crystal_id
_definition.id '_diffrn_refln.crystal_id'
loop_
_alias.definition_id
'_diffrn_refln.crystal_id'
'_diffrn_refln_crystal_id'
_definition.update 2012-11-26
_description.text
;
Code identifying each crystal if multiple crystals are used.
;
_name.category_id diffrn_refln
_name.object_id crystal_id
_name.linked_item_id '_exptl_crystal.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save__diffrn_refln.detect_slit_horiz
_definition.id '_diffrn_refln.detect_slit_horiz'
loop_
_alias.definition_id
'_diffrn_refln.detect_slit_horiz'
'_diffrn_refln_detect_slit_horiz'
_definition.update 2012-11-26
_description.text
;
Total slit aperture angle in the diffraction plane.
;
_name.category_id diffrn_refln
_name.object_id detect_slit_horiz
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:90.0
_units.code degrees
save_
save__diffrn_refln.detect_slit_vert
_definition.id '_diffrn_refln.detect_slit_vert'
loop_
_alias.definition_id
'_diffrn_refln.detect_slit_vert'
'_diffrn_refln_detect_slit_vert'
_definition.update 2012-11-26
_description.text
;
Total slit aperture angle perpendicular to the diffraction plane.
;
_name.category_id diffrn_refln
_name.object_id detect_slit_vert
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:90.0
_units.code degrees
save_
save__diffrn_refln.elapsed_time
_definition.id '_diffrn_refln.elapsed_time'
loop_
_alias.definition_id
'_diffrn_refln.elapsed_time'
'_diffrn_refln_elapsed_time'
_definition.update 2012-11-26
_description.text
;
Elapsed time from the start to the end of the intensity measurement.
;
_name.category_id diffrn_refln
_name.object_id elapsed_time
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code minutes
save_
save__diffrn_refln.hkl
_definition.id '_diffrn_refln.hkl'
loop_
_alias.definition_id
'_diffrn_refln.hkl'
_definition.update 2012-11-26
_description.text
;
Miller indices of a measured reflection. These need not match the
_refln.hkl values if a transformation of the original measured
cell has taken place.
;
_name.category_id diffrn_refln
_name.object_id hkl
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Integer
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With a as diffrn_refln
_diffrn_refln.hkl = [a.index_h, a.index_h, a.index_l]
;
save_
save__diffrn_refln.index_h
_definition.id '_diffrn_refln.index_h'
loop_
_alias.definition_id
'_diffrn_refln.index_h'
'_diffrn_refln_index_h'
_name.category_id diffrn_refln
_name.object_id index_h
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__diffrn_refln.index_k
_definition.id '_diffrn_refln.index_k'
loop_
_alias.definition_id
'_diffrn_refln.index_k'
'_diffrn_refln_index_k'
_name.category_id diffrn_refln
_name.object_id index_k
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__diffrn_refln.index_l
_definition.id '_diffrn_refln.index_l'
loop_
_alias.definition_id
'_diffrn_refln.index_l'
'_diffrn_refln_index_l'
_name.category_id diffrn_refln
_name.object_id index_l
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__diffrn_refln.intensity_net
_definition.id '_diffrn_refln.intensity_net'
loop_
_alias.definition_id
'_diffrn_refln.intensity_net'
'_diffrn_refln_intensity_net'
_definition.update 2012-11-26
_description.text
;
Net intensity calculated from the diffraction counts after the
attenuator and standard scales have been applied.
;
_name.category_id diffrn_refln
_name.object_id intensity_net
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0:
_units.code none
save_
save__diffrn_refln.intensity_net_su
_definition.id '_diffrn_refln.intensity_net_su'
loop_
_alias.definition_id
'_diffrn_refln.intensity_net_su'
'_diffrn_refln_intensity_u'
'_diffrn_refln_intensity_sigma'
'_diffrn_refln.intensity_sigma'
'_diffrn_refln.intensity_u'
_definition.update 2012-12-13
_description.text
;
Standard uncertainty of the net intensity calculated from the
diffraction counts after the attenuator and standard scales
have been applied.
;
_name.category_id diffrn_refln
_name.object_id intensity_net_su
_name.linked_item_id '_diffrn_refln.intensity_net'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0:
_units.code none
save_
save__diffrn_refln.key
_definition.id '_diffrn_refln.key'
loop_
_alias.definition_id
'_diffrn_refln.key'
_definition.update 2012-11-26
_description.text
;
Value is a unique key to a set of DIFFRN_REFLN items
in a looped list.
;
_name.category_id diffrn_refln
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Matrix
_type.contents Integer
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation ' _diffrn_refln.key = _diffrn_refln.hkl'
save_
save__diffrn_refln.scale_group_code
_definition.id '_diffrn_refln.scale_group_code'
loop_
_alias.definition_id
'_diffrn_refln.scale_group_code'
'_diffrn_refln_scale_group_code'
_definition.update 2012-11-26
_description.text
;
Code identifying the scale applying to this reflection.
;
_name.category_id diffrn_refln
_name.object_id scale_group_code
_name.linked_item_id '_diffrn_scale_group.code'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save__diffrn_refln.scan_mode
_definition.id '_diffrn_refln.scan_mode'
loop_
_alias.definition_id
'_diffrn_refln.scan_mode'
'_diffrn_refln_scan_mode'
_definition.update 2012-11-26
_description.text
;
Code identifying the mode of scanning with a diffractometer.
See also _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd.
;
_name.category_id diffrn_refln
_name.object_id scan_mode
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
om 'omega scan'
ot 'omega/2theta scan'
q 'Q-scans (arbitrary reciprocal directions)'
_enumeration.default ot
save_
save__diffrn_refln.scan_mode_backgd
_definition.id '_diffrn_refln.scan_mode_backgd'
loop_
_alias.definition_id
'_diffrn_refln.scan_mode_backgd'
'_diffrn_refln_scan_mode_backgd'
_definition.update 2012-11-26
_description.text
;
Code identifying mode of scanning to measure the background intensity.
;
_name.category_id diffrn_refln
_name.object_id scan_mode_backgd
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
st 'stationary counter background'
mo 'moving counter background'
_enumeration.default st
save_
save__diffrn_refln.scan_rate
_definition.id '_diffrn_refln.scan_rate'
loop_
_alias.definition_id
'_diffrn_refln.scan_rate'
'_diffrn_refln_scan_rate'
_definition.update 2013-03-07
_description.text
;
Angular rate of scanning a reflection to measure the intensity.
;
_name.category_id diffrn_refln
_name.object_id scan_rate
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code degree_per_minute
save_
save__diffrn_refln.scan_time_backgd
_definition.id '_diffrn_refln.scan_time_backgd'
loop_
_alias.definition_id
'_diffrn_refln.scan_time_backgd'
'_diffrn_refln_scan_time_backgd'
_definition.update 2012-11-26
_description.text
;
Time spent measuring background counts.
;
_name.category_id diffrn_refln
_name.object_id scan_time_backgd
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code seconds
save_
save__diffrn_refln.scan_width
_definition.id '_diffrn_refln.scan_width'
loop_
_alias.definition_id
'_diffrn_refln.scan_width'
'_diffrn_refln_scan_width'
_definition.update 2012-11-26
_description.text
;
Angular scan width when measuring the peak intensity.
;
_name.category_id diffrn_refln
_name.object_id scan_width
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:90.0
_units.code degrees
save_
save__diffrn_refln.sin_theta_over_lambda
_definition.id '_diffrn_refln.sin_theta_over_lambda'
loop_
_alias.definition_id
'_diffrn_refln.sin_theta_over_lambda'
'_diffrn_refln_sint/lambda'
'_diffrn_refln_sint_over_lambda'
'_diffrn_refln.sint_over_lambda'
_definition.update 2012-11-26
_description.text
;
(sin theta)/lambda value for this reflection.
;
_name.category_id diffrn_refln
_name.object_id sin_theta_over_lambda
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code reciprocal_angstroms
save_
save__diffrn_refln.standard_code
_definition.id '_diffrn_refln.standard_code'
loop_
_alias.definition_id
'_diffrn_refln.standard_code'
'_diffrn_refln_standard_code'
_definition.update 2012-11-26
_description.text
;
Code identifying reflections measured repeated as standard intensity.
Must match a _diffrn_standard_refln.code values OR set to '.' if
it was not used as a intensity standard.
;
_name.category_id diffrn_refln
_name.object_id standard_code
_name.linked_item_id '_diffrn_standard_refln.code'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save__diffrn_refln.wavelength
_definition.id '_diffrn_refln.wavelength'
loop_
_alias.definition_id
'_diffrn_refln.wavelength'
'_diffrn_refln_wavelength'
_definition.update 2012-11-26
_description.text
;
Mean wavelength of radiation used to measure this intensity.
;
_name.category_id diffrn_refln
_name.object_id wavelength
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__diffrn_refln.wavelength_id
_definition.id '_diffrn_refln.wavelength_id'
loop_
_alias.definition_id
'_diffrn_refln.wavelength_id'
'_diffrn_refln_wavelength_id'
_definition.update 2012-11-26
_description.text
;
Code identifying the wavelength in the diffrn_radiation_wavelength list.
;
_name.category_id diffrn_refln
_name.object_id wavelength_id
_name.linked_item_id '_diffrn_radiation_wavelength.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save_DIFFRN_REFLNS
_definition.id DIFFRN_REFLNS
_definition.scope Category
_definition.class Set
_definition.update 2012-11-26
_description.text
;
The CATEGORY of data items which specify the overall reflection
measurement information.
;
_name.category_id DIFFRN
_name.object_id DIFFRN_REFLNS
save_
save__diffrn_reflns.av_R_equivalents
_definition.id '_diffrn_reflns.av_R_equivalents'
loop_
_alias.definition_id
'_diffrn_reflns.av_R_equivalents'
'_diffrn_reflns_av_R_equivalents'
_definition.update 2012-11-26
_description.text
;
The residual [sum av|del(I)| / sum |av(I)|] for symmetry-equivalent
reflections used to calculate the average intensity av(I). The
av|del(I)| term is the average absolute difference between av(I) and
the individual symmetry-equivalent intensities.
;
_name.category_id diffrn_reflns
_name.object_id av_R_equivalents
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__diffrn_reflns.av_sunetI_over_netI
_definition.id '_diffrn_reflns.av_sunetI_over_netI'
loop_
_alias.definition_id
'_diffrn_reflns.av_sunetI_over_netI'
'_diffrn_reflns_av_sigmaI_over_netI'
'_diffrn_reflns_av_sigmaI/netI'
'_diffrn_reflns.av_unetI/netI'
'_diffrn_reflns_av_unetI/netI'
'_diffrn_reflns.av_sigmaI_over_netI'
_definition.update 2012-11-26
_description.text
;
Recorded [sum |su(netI)| / sum |netI|] for all measured reflections.
;
_name.category_id diffrn_reflns
_name.object_id av_sunetI_over_netI
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__diffrn_reflns.Laue_measured_fraction_full
_definition.id '_diffrn_reflns.Laue_measured_fraction_full'
loop_
_alias.definition_id
'_diffrn_reflns.Laue_measured_fraction_full'
'_diffrn_reflns_Laue_measured_fraction_full'
_definition.update 2013-01-20
_description.text
;
Fraction of Laue_group unique reflections (symmetry-independent in
the Laue group) measured out to the resolution given in
_diffrn_reflns.resolution_full or _diffrn_reflns.theta_full.
The Laue group always contains a centre of symmetry so that
the reflection h,k,l is always equivalent to the reflection
-h,-k,-l even in space groups without a centre of symmetry.
This number should not be less than 0.95, since it represents
the fraction of reflections measured in the part of the
diffraction pattern that is essentially complete.
;
_name.category_id diffrn_reflns
_name.object_id Laue_measured_fraction_full
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.95:1.0
_units.code none
save_
save__diffrn_reflns.Laue_measured_fraction_max
_definition.id '_diffrn_reflns.Laue_measured_fraction_max'
loop_
_alias.definition_id
'_diffrn_reflns.Laue_measured_fraction_max'
'_diffrn_reflns_Laue_measured_fraction_max'
_definition.update 2013-01-20
_description.text
;
Fraction of Laue-group unique reflections (symmetry-independent in
the Laue group) measured out to the resolution given in
_diffrn_reflns.resolution_max or _diffrn_reflns.theta_max.
The Laue group always contains a centre of symmetry so that the
reflection h,k,l is always equivalent to the reflection -h,-k,-l
even in space groups without a centre of symmetry.
;
_name.category_id diffrn_reflns
_name.object_id Laue_measured_fraction_max
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save__diffrn_reflns.limit_h_max
_definition.id '_diffrn_reflns.limit_h_max'
loop_
_alias.definition_id
'_diffrn_reflns.limit_h_max'
'_diffrn_reflns_limit_h_max'
_name.category_id diffrn_reflns
_name.object_id limit_h_max
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__diffrn_reflns.limit_h_min
_definition.id '_diffrn_reflns.limit_h_min'
loop_
_alias.definition_id
'_diffrn_reflns.limit_h_min'
'_diffrn_reflns_limit_h_min'
_name.category_id diffrn_reflns
_name.object_id limit_h_min
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__diffrn_reflns.limit_k_max
_definition.id '_diffrn_reflns.limit_k_max'
loop_
_alias.definition_id
'_diffrn_reflns.limit_k_max'
'_diffrn_reflns_limit_k_max'
_name.category_id diffrn_reflns
_name.object_id limit_k_max
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__diffrn_reflns.limit_k_min
_definition.id '_diffrn_reflns.limit_k_min'
loop_
_alias.definition_id
'_diffrn_reflns.limit_k_min'
'_diffrn_reflns_limit_k_min'
_name.category_id diffrn_reflns
_name.object_id limit_k_min
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__diffrn_reflns.limit_l_max
_definition.id '_diffrn_reflns.limit_l_max'
loop_
_alias.definition_id
'_diffrn_reflns.limit_l_max'
'_diffrn_reflns_limit_l_max'
_name.category_id diffrn_reflns
_name.object_id limit_l_max
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__diffrn_reflns.limit_l_min
_definition.id '_diffrn_reflns.limit_l_min'
loop_
_alias.definition_id
'_diffrn_reflns.limit_l_min'
'_diffrn_reflns_limit_l_min'
_name.category_id diffrn_reflns
_name.object_id limit_l_min
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__diffrn_reflns.limit_max
_definition.id '_diffrn_reflns.limit_max'
loop_
_alias.definition_id
'_diffrn_reflns.limit_max'
_definition.update 2013-01-15
_description.text
;
Maximum Miller indices of measured diffraction reflections.
;
_name.category_id diffrn_reflns
_name.object_id limit_max
_type.purpose Number
_type.source Assigned
_type.container Matrix
_type.contents Real
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With t as diffrn_reflns
_diffrn_reflns.limit_max = [t.limit_h_max,t.limit_k_max,t.limit_l_max]
;
save_
save__diffrn_reflns.limit_min
_definition.id '_diffrn_reflns.limit_min'
loop_
_alias.definition_id
'_diffrn_reflns.limit_min'
_definition.update 2013-01-15
_description.text
;
Minimum Miller indices of meas.ued diffraction reflections.
;
_name.category_id diffrn_reflns
_name.object_id limit_min
_type.purpose Number
_type.source Assigned
_type.container Matrix
_type.contents Real
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With t as diffrn_reflns
_diffrn_reflns.limit_min = [t.limit_h_min,t.limit_k_min,t.limit_l_min]
;
save_
save__diffrn_reflns.number
_definition.id '_diffrn_reflns.number'
loop_
_alias.definition_id
'_diffrn_reflns.number'
'_diffrn_reflns_number'
_definition.update 2012-11-26
_description.text
;
Total number of measured intensities, excluding reflections that are
classed as systematically absent arising from translational symmetry
in the crystal unit cell.
;
_name.category_id diffrn_reflns
_name.object_id number
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save__diffrn_reflns.point_measured_fraction_full
_definition.id '_diffrn_reflns.point_measured_fraction_full'
loop_
_alias.definition_id
'_diffrn_reflns.point_measured_fraction_full'
"ffrn_reflns_point_group_measured_fraction_full'"
_definition.update 2013-01-20
_description.text
;
Fraction of crystal point-group unique reflections (i.e.
symmetry-independent in the crystal point group) measured
out to the resolution given in _diffrn_reflns.resolution_full
or _diffrn_reflns.theta_full. For space groups that do not
contain a centre of symmetry the reflections h,k,l and
-h,-k,-l are independent. This number should not be less
than 0.95, since it represents the fraction of reflections
measured in the part of the diffraction pattern that is
essentially complete.
;
_name.category_id diffrn_reflns
_name.object_id point_measured_fraction_full
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.95:1.0
_units.code none
save_
save__diffrn_reflns.point_measured_fraction_max
_definition.id '_diffrn_reflns.point_measured_fraction_max'
loop_
_alias.definition_id
'_diffrn_reflns.point_measured_fraction_max'
"ffrn_reflns_point_group_measured_fraction_max'"
_definition.update 2013-01-20
_description.text
;
Fraction of crystal point-group unique reflections (i.e.
symmetry-independent in the crystal point group) measured
out to the resolution given in _diffrn_reflns.resolution_max
or _diffrn_reflns.theta_max. For space groups that do not
contain a centre of symmetry the reflections h,k,l and
-h,-k,-l are independent.
;
_name.category_id diffrn_reflns
_name.object_id point_measured_fraction_max
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.95:1.0
_units.code none
save_
save__diffrn_reflns.reduction_process
_definition.id '_diffrn_reflns.reduction_process'
loop_
_alias.definition_id
'_diffrn_reflns.reduction_process'
'_diffrn_reflns_reduction_process'
_definition.update 2012-11-26
_description.text
;
How intensities were reduced to structure-factor magnitudes.
;
_name.category_id diffrn_reflns
_name.object_id reduction_process
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'data averaged using Fisher test'
save_
save__diffrn_reflns.resolution_full
_definition.id '_diffrn_reflns.resolution_full'
loop_
_alias.definition_id
'_diffrn_reflns.resolution_full'
'_diffrn_reflns_resolution_full'
_definition.update 2012-11-26
_description.text
;
The resolution at which the measured reflection count is close
to complete. The fraction of unique reflections measured out
to this angle is given by _diffrn.measured_fraction_theta_full.
;
_name.category_id diffrn_reflns
_name.object_id resolution_full
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code reciprocal_angstroms
save_
save__diffrn_reflns.resolution_max
_definition.id '_diffrn_reflns.resolution_max'
loop_
_alias.definition_id
'_diffrn_reflns.resolution_max'
'_diffrn_reflns_resolution_max'
_definition.update 2013-02-22
_description.text
;
Maximum resolution of the measured diffraction pattern.
The fraction of unique reflections measured out to this angle
is given by _diffrn.measured_fraction_theta_max.
;
_name.category_id diffrn_reflns
_name.object_id resolution_max
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code reciprocal_angstroms
save_
save__diffrn_reflns.theta_full
_definition.id '_diffrn_reflns.theta_full'
loop_
_alias.definition_id
'_diffrn_reflns.theta_full'
'_diffrn_reflns_theta_full'
_definition.update 2012-11-26
_description.text
;
Theta angle at which the count of measured reflections is almost
complete. The fraction of unique reflections measured out to
this angle is given by _diffrn.measured_fraction_theta_full.
;
_name.category_id diffrn_reflns
_name.object_id theta_full
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:90.0
_units.code degrees
save_
save__diffrn_reflns.theta_max
_definition.id '_diffrn_reflns.theta_max'
loop_
_alias.definition_id
'_diffrn_reflns.theta_max'
'_diffrn_reflns_theta_max'
_definition.update 2012-11-26
_description.text
;
Maximum theta angle of the measured reflections.
;
_name.category_id diffrn_reflns
_name.object_id theta_max
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:90.0
_units.code degrees
save_
save__diffrn_reflns.theta_min
_definition.id '_diffrn_reflns.theta_min'
loop_
_alias.definition_id
'_diffrn_reflns.theta_min'
'_diffrn_reflns_theta_min'
_definition.update 2012-11-26
_description.text
;
Minimum theta angle of the measured reflections.
;
_name.category_id diffrn_reflns
_name.object_id theta_min
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:90.0
_units.code degrees
save_
save_DIFFRN_REFLNS_CLASS
_definition.id DIFFRN_REFLNS_CLASS
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items which specify different classes of
reflections in the raw measured diffraction data.
;
_name.category_id DIFFRN_REFLNS
_name.object_id DIFFRN_REFLNS_CLASS
_category.key_id '_diffrn_reflns_class.key'
_category.key_list ['_diffrn_reflns_class.code']
save_
save__diffrn_reflns_class.av_R_eq
_definition.id '_diffrn_reflns_class.av_R_eq'
loop_
_alias.definition_id
'_diffrn_reflns_class.av_R_eq'
'_diffrn_reflns_class_av_R_eq'
_definition.update 2012-11-26
_description.text
;
Residual [sum av|del(I)|/sum|av(I)|] for symmetry-equivalent
reflections used to calculate the average intensity av(I).
The av|del(I)| term is the average absolute difference
between av(I) and the individual intensities.
;
_name.category_id diffrn_reflns_class
_name.object_id av_R_eq
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__diffrn_reflns_class.av_suI_over_I
_definition.id '_diffrn_reflns_class.av_suI_over_I'
loop_
_alias.definition_id
'_diffrn_reflns_class.av_suI_over_I'
'_diffrn_reflns_class_av_uI_over_I'
'_diffrn_reflns_class.av_uI/I'
'_diffrn_reflns_class_av_uI/I'
'_diffrn_reflns_class.av_sgI/I'
'_diffrn_reflns_class_av_sgI/I'
_definition.update 2014-07-22
_description.text
;
Recorded [sum|su(net I)|/sum|net I|] in a reflection class.
;
_name.category_id diffrn_reflns_class
_name.object_id av_suI_over_I
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__diffrn_reflns_class.code
_definition.id '_diffrn_reflns_class.code'
loop_
_alias.definition_id
'_diffrn_reflns_class.code'
'_diffrn_reflns_class_code'
_definition.update 2012-11-26
_description.text
;
Code identifying a reflection class.
;
_name.category_id diffrn_reflns_class
_name.object_id code
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_description_example.case
m2
save_
save__diffrn_reflns_class.d_res_high
_definition.id '_diffrn_reflns_class.d_res_high'
loop_
_alias.definition_id
'_diffrn_reflns_class.d_res_high'
'_diffrn_reflns_class_d_res_high'
_definition.update 2012-11-26
_description.text
;
Highest resolution in reflection class i.e. smallest d value in class.
;
_name.category_id diffrn_reflns_class
_name.object_id d_res_high
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__diffrn_reflns_class.d_res_low
_definition.id '_diffrn_reflns_class.d_res_low'
loop_
_alias.definition_id
'_diffrn_reflns_class.d_res_low'
'_diffrn_reflns_class_d_res_low'
_definition.update 2012-11-26
_description.text
;
Lowest resolution in reflection class i.e. largest d value in class.
;
_name.category_id diffrn_reflns_class
_name.object_id d_res_low
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__diffrn_reflns_class.description
_definition.id '_diffrn_reflns_class.description'
loop_
_alias.definition_id
'_diffrn_reflns_class.description'
'_diffrn_reflns_class_description'
_definition.update 2012-11-26
_description.text
;
Description of a reflection class.
;
_name.category_id diffrn_reflns_class
_name.object_id description
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'm=1 first order satellites'
save_
save__diffrn_reflns_class.key
_definition.id '_diffrn_reflns_class.key'
loop_
_alias.definition_id
'_diffrn_reflns_class.key'
_definition.update 2012-11-26
_description.text
;
Value is a unique key to a set of DIFFRN_REFLNS_CLASS items
in a looped list.
;
_name.category_id diffrn_reflns_class
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _diffrn_reflns_class.key = _diffrn_reflns_class.code'
save_
save__diffrn_reflns_class.number
_definition.id '_diffrn_reflns_class.number'
loop_
_alias.definition_id
'_diffrn_reflns_class.number'
'_diffrn_reflns_class_number'
_definition.update 2012-11-26
_description.text
;
Number of measured intensities for a reflection class, excluding
the systematic absences arising from centring translations.
;
_name.category_id diffrn_reflns_class
_name.object_id number
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save_DIFFRN_REFLNS_TRANSF_MATRIX
_definition.id DIFFRN_REFLNS_TRANSF_MATRIX
_definition.scope Category
_definition.class Set
_definition.update 2012-11-26
_description.text
;
The CATEGORY of data items which specify the elements of the matrix
used to transform the reflection indices _diffrn_refln.hkl
into _refln.hkl.
|11 12 13|
(h k l) diffraction |21 22 23| = (h' k' l')
|31 32 33|
;
_name.category_id DIFFRN_REFLNS
_name.object_id DIFFRN_REFLNS_TRANSF_MATRIX
save_
save__diffrn_reflns_transf_matrix.11
_definition.id '_diffrn_reflns_transf_matrix.11'
loop_
_alias.definition_id
'_diffrn_reflns_transf_matrix.11'
'_diffrn_reflns_transf_matrix_11'
'_diffrn_reflns.transf_matrix[1][1]'
_name.category_id diffrn_reflns_transf_matrix
_name.object_id 11
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix
used to transform the reflection indices _diffrn_refln.hkl
into _refln.hkl.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_reflns_transf_matrix.12
_definition.id '_diffrn_reflns_transf_matrix.12'
loop_
_alias.definition_id
'_diffrn_reflns_transf_matrix.12'
'_diffrn_reflns_transf_matrix_12'
'_diffrn_reflns.transf_matrix[1][2]'
_name.category_id diffrn_reflns_transf_matrix
_name.object_id 12
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix
used to transform the reflection indices _diffrn_refln.hkl
into _refln.hkl.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_reflns_transf_matrix.13
_definition.id '_diffrn_reflns_transf_matrix.13'
loop_
_alias.definition_id
'_diffrn_reflns_transf_matrix.13'
'_diffrn_reflns_transf_matrix_13'
'_diffrn_reflns.transf_matrix[1][3]'
_name.category_id diffrn_reflns_transf_matrix
_name.object_id 13
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix
used to transform the reflection indices _diffrn_refln.hkl
into _refln.hkl.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_reflns_transf_matrix.21
_definition.id '_diffrn_reflns_transf_matrix.21'
loop_
_alias.definition_id
'_diffrn_reflns_transf_matrix.21'
'_diffrn_reflns_transf_matrix_21'
'_diffrn_reflns.transf_matrix[2][1]'
_name.category_id diffrn_reflns_transf_matrix
_name.object_id 21
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix
used to transform the reflection indices _diffrn_refln.hkl
into _refln.hkl.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_reflns_transf_matrix.22
_definition.id '_diffrn_reflns_transf_matrix.22'
loop_
_alias.definition_id
'_diffrn_reflns_transf_matrix.22'
'_diffrn_reflns_transf_matrix_22'
'_diffrn_reflns.transf_matrix[2][2]'
_name.category_id diffrn_reflns_transf_matrix
_name.object_id 22
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix
used to transform the reflection indices _diffrn_refln.hkl
into _refln.hkl.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_reflns_transf_matrix.23
_definition.id '_diffrn_reflns_transf_matrix.23'
loop_
_alias.definition_id
'_diffrn_reflns_transf_matrix.23'
'_diffrn_reflns_transf_matrix_23'
'_diffrn_reflns.transf_matrix[2][3]'
_name.category_id diffrn_reflns_transf_matrix
_name.object_id 23
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix
used to transform the reflection indices _diffrn_refln.hkl
into _refln.hkl.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_reflns_transf_matrix.31
_definition.id '_diffrn_reflns_transf_matrix.31'
loop_
_alias.definition_id
'_diffrn_reflns_transf_matrix.31'
'_diffrn_reflns_transf_matrix_31'
'_diffrn_reflns.transf_matrix[3][1]'
_name.category_id diffrn_reflns_transf_matrix
_name.object_id 31
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix
used to transform the reflection indices _diffrn_refln.hkl
into _refln.hkl.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_reflns_transf_matrix.32
_definition.id '_diffrn_reflns_transf_matrix.32'
loop_
_alias.definition_id
'_diffrn_reflns_transf_matrix.32'
'_diffrn_reflns_transf_matrix_32'
'_diffrn_reflns.transf_matrix[3][2]'
_name.category_id diffrn_reflns_transf_matrix
_name.object_id 32
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix
used to transform the reflection indices _diffrn_refln.hkl
into _refln.hkl.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_reflns_transf_matrix.33
_definition.id '_diffrn_reflns_transf_matrix.33'
loop_
_alias.definition_id
'_diffrn_reflns_transf_matrix.33'
'_diffrn_reflns_transf_matrix_33'
'_diffrn_reflns.transf_matrix[3][3]'
_name.category_id diffrn_reflns_transf_matrix
_name.object_id 33
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items which specify the elements of the matrix
used to transform the reflection indices _diffrn_refln.hkl
into _refln.hkl.
;
_enumeration.default ?
_type.source Recorded
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__diffrn_reflns_transf_matrix.TIJ
_definition.id '_diffrn_reflns_transf_matrix.TIJ'
loop_
_alias.definition_id
'_diffrn_reflns_transf_matrix.TIJ'
_definition.update 2012-11-26
_description.text
;
Elements of the matrix used to transform the diffraction reflection
indices _diffrn_refln.hkl into the _refln.hkl indices.
|11 12 13|
(h k l) diffraction |21 22 23| = (h' k' l')
|31 32 33|
;
_name.category_id diffrn_reflns_transf_matrix
_name.object_id TIJ
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3 3]
loop_
_method.purpose
_method.expression
Evaluation
;
With t as diffrn_reflns_transf_matrix
_diffrn_reflns_transf_matrix.TIJ = [[t.11, t.12, t.13],
[t.21, t.22, t.23],
[t.31, t.32, t.33]]
;
save_
save_DIFFRN_SCALE_GROUP
_definition.id DIFFRN_SCALE_GROUP
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items which specify the groups of reflections in
the raw measured diffraction data with different relative scales.
;
_name.category_id DIFFRN
_name.object_id DIFFRN_SCALE_GROUP
_category.key_id '_diffrn_scale_group.key'
_category.key_list ['_diffrn_scale_group.code']
save_
save__diffrn_scale_group.code
_definition.id '_diffrn_scale_group.code'
loop_
_alias.definition_id
'_diffrn_scale_group.code'
'_diffrn_scale_group_code'
_definition.update 2012-11-26
_description.text
;
Code identifying a specific scale group of reflections (e.g. for
multi-film or multi-crystal data). The code must match a
_diffrn_refln.scale_group_code in the diffrn_refln list.
;
_name.category_id diffrn_scale_group
_name.object_id code
_name.linked_item_id '_diffrn_refln.scale_group_code'
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_description_example.case
1
2
3
s1
A
B
c1
c2
c3
save_
save__diffrn_scale_group.I_net
_definition.id '_diffrn_scale_group.I_net'
loop_
_alias.definition_id
'_diffrn_scale_group.I_net'
'_diffrn_scale_group_I_net'
_definition.update 2012-11-26
_description.text
;
Scale for a specific measurement group of eflections. Is multiplied
with the net intensity to place all intensities on a common scale.
;
_name.category_id diffrn_scale_group
_name.object_id I_net
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__diffrn_scale_group.key
_definition.id '_diffrn_scale_group.key'
loop_
_alias.definition_id
'_diffrn_scale_group.key'
_definition.update 2012-11-26
_description.text
;
Value is a unique key to a set of DIFFRN_SCALE_GROUP items
in a looped list.
;
_name.category_id diffrn_scale_group
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _diffrn_scale_group.key = _diffrn_scale_group.code'
save_
save_DIFFRN_SOURCE
_definition.id DIFFRN_SOURCE
_definition.scope Category
_definition.class Set
_definition.update 2012-11-26
_description.text
;
The CATEGORY of data items which specify information about the
radiation source.
;
_name.category_id DIFFRN
_name.object_id DIFFRN_SOURCE
save_
save__diffrn_source.current
_definition.id '_diffrn_source.current'
loop_
_alias.definition_id
'_diffrn_source.current'
'_diffrn_source_current'
_definition.update 2012-11-26
_description.text
;
Generator current at which the radiation source device was operated.
;
_name.category_id diffrn_source
_name.object_id current
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code milliamperes
save_
save__diffrn_source.details
_definition.id '_diffrn_source.details'
loop_
_alias.definition_id
'_diffrn_source.details'
'_diffrn_source_details'
_definition.update 2012-11-26
_description.text
;
General description of the radiation source device.
;
_name.category_id diffrn_source
_name.object_id details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__diffrn_source.device
_definition.id '_diffrn_source.device'
loop_
_alias.definition_id
'_diffrn_source.device'
'_diffrn_source'
'_diffrn_radiation_source'
'_diffrn_source.source'
_definition.update 2013-08-09
_description.text
;
Enumerated code for the device providing the source of radiation.
;
_name.category_id diffrn_source
_name.object_id device
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
tube 'sealed X-ray tube'
nuclear 'nuclear reactor'
spallation 'spallation source'
elect-micro 'electron microscope'
rot_anode 'rotating-anode X-ray tube'
synch synchrotron
_enumeration.default tube
save_
save__diffrn_source.make
_definition.id '_diffrn_source.make'
loop_
_alias.definition_id
'_diffrn_source.make'
'_diffrn_source_make'
'_diffrn_source.type'
'_diffrn_source_type'
_definition.update 2012-11-26
_description.text
;
Description of the make, model or name of the source device.
;
_name.category_id diffrn_source
_name.object_id make
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'NSLS beamline X8C'
'Rigaku RU2012-05-07 '
save_
save__diffrn_source.power
_definition.id '_diffrn_source.power'
loop_
_alias.definition_id
'_diffrn_source.power'
'_diffrn_source_power'
_definition.update 2012-11-26
_description.text
' Generator power at which the radiation source device was operated.'
_name.category_id diffrn_source
_name.object_id power
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kilowatts
save_
save__diffrn_source.size
_definition.id '_diffrn_source.size'
loop_
_alias.definition_id
'_diffrn_source.size'
'_diffrn_source_size'
_definition.update 2012-11-26
_description.text
;
Description of the collimated source beam as viewed from the sample.
;
_name.category_id diffrn_source
_name.object_id size
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'8mm x 0.4 mm fine-focus'
'broad focus'
save_
save__diffrn_source.take_off_angle
_definition.id '_diffrn_source.take_off_angle'
loop_
_alias.definition_id
'_diffrn_source.take_off_angle'
'_diffrn_source_take-off_angle'
'_diffrn_source.take-off_angle'
_definition.update 2013-02-22
_description.text
;
The complement of the angle in degrees between the normal
to the surface of the X-ray tube target and the primary
X-ray beam for beams generated by traditional X-ray tubes.
;
_name.category_id diffrn_source
_name.object_id take_off_angle
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0:90
_units.code degrees
save_
save__diffrn_source.target
_definition.id '_diffrn_source.target'
loop_
_alias.definition_id
'_diffrn_source.target'
'_diffrn_source_target'
_definition.update 2012-11-26
_description.text
;
Chemical element symbol for the radiation source target (usually
the anode). This can be used also for spallation sources.
;
_name.category_id diffrn_source
_name.object_id target
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
_enumeration.default Cu
loop_
_enumeration_set.state
_enumeration_set.detail
Ac Actinium
Ag Silver
Al Aluminum
Am Americium
Ar Argon
As Arsenic
At Astatine
Au Gold
B Boron
Ba Barium
Be Beryllium
Bh Bohrium
Bi Bismuth
Bk Berkelium
Br Bromine
C Carbon
Ca Calcium
Cd Cadmium
Ce Cerium
Cf Californium
Cl Chlorine
Cm Curium
Co Cobalt
Cr Chromium
Cs Cesium
Cu Copper
Db Dubnium
Ds Darmstadtium
Dy Dysprosium
Er Erbium
Es Einsteinium
Eu Europium
F Fluorine
Fe Iron
Fm Fermium
Fr Francium
Ga Gallium
Gd Gadolinium
Ge Germanium
H Hydrogen
He Helium
Hf Hafnium
Hg Mercury
Ho Holmium
Hs Hassium
I Iodine
In Indium
Ir Iridium
K Potassium
Kr Krypton
La Lanthanum
Li Lithium
Lr Lawrencium
Lu Lutetium
Md Mendelevium
Mg Magnesium
Mn Manganese
Mo Molybdenum
Mt Meitnerium
N Nitrogen
Na Sodium
Ne Neon
Nb Niobium
Nd Neodymium
Ni Nickel
No Nobelium
Np Neptunium
O Oxygen
Os Osmium
P Phosphorus
Pd Palladium
Po Polonium
Pb Lead
Pt Platinum
Pr Praseodymium
Pm Promethium
Pu Plutonium
Pa Protactinium
Ra Radium
Rb Rubidium
Re Rhenium
Rf Rutherfordium
Rh Rhodium
Rn Radon
Ru Ruthenium
S Sulfur
Sb Antimony
Sc Scandium
Se Selenium
Sg Seaborgium
Si Silicon
Sm Samarium
Sn Tin
Sr Strontium
Ta Tantalum
Tb Terbium
Tc Technetium
Te Tellurium
Th Thorium
Ti Titanium
Tl Thallium
Tm Thulium
U Uranium
Uub Ununbium
Uun Ununnilium
Uuu Ununumium
V Vanadium
W Tungsten
Xe Xenon
Y Yttrium
Yb Ytterbium
Zn Zinc
Zr Zirconium
save_
save__diffrn_source.voltage
_definition.id '_diffrn_source.voltage'
loop_
_alias.definition_id
'_diffrn_source.voltage'
'_diffrn_source_voltage'
_definition.update 2012-11-26
_description.text
;
Generator voltage at which the radiation source device was operated.
;
_name.category_id diffrn_source
_name.object_id voltage
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kilovolts
save_
save_DIFFRN_STANDARD
_definition.id DIFFRN_STANDARD
_definition.scope Category
_definition.class Set
_definition.update 2012-11-26
_description.text
;
The CATEGORY of data items which specify information about the
standard reflections used in the diffraction measurement process.
;
_name.category_id DIFFRN
_name.object_id DIFFRN_STANDARD
save_
save__diffrn_standard.decay_percent
_definition.id '_diffrn_standard.decay_percent'
loop_
_alias.definition_id
'_diffrn_standard.decay_percent'
'_diffrn_standards_decay_%'
'_diffrn_standards.decay_%'
'_diffrn_standards_decay_percent'
_definition.update 2013-03-07
_description.text
;
The percentage decrease in the mean of the intensities for the
standard reflections at the start to the finish of the measurement
process. This value affords a measure of the overall decay in
crystal quality during measurement. Negative values only occur in
exceptional instances where the final intensities are greater than
the initial ones. If no measurable decay has occurred, the
standard uncertainty should be quoted to indicate the maximum
possible value the decay might have. A range of 3 standard
uncertainties is considered possible. Thus 0.0(1) would indicate
a decay of less than 0.3% or an enhancement of less than 0.3%.
;
_name.category_id diffrn_standard
_name.object_id decay_percent
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range :100
_units.code none
loop_
_description_example.case
_description_example.detail
0.5(1) 'represents a decay between 0.2% and 0.8%'
-1(1) 'change in standards between 2% decay and 4% rise'
0.0(2) 'change in standards between 0.6% decay and 0.6% rise.'
save_
save__diffrn_standard.interval_count
_definition.id '_diffrn_standard.interval_count'
loop_
_alias.definition_id
'_diffrn_standard.interval_count'
'_diffrn_standards_interval_count'
'_diffrn_standards.interval_count'
_definition.update 2012-11-26
_description.text
;
Reflection count between the standard reflection measurements.
;
_name.category_id diffrn_standard
_name.object_id interval_count
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save__diffrn_standard.interval_time
_definition.id '_diffrn_standard.interval_time'
loop_
_alias.definition_id
'_diffrn_standard.interval_time'
'_diffrn_standards_interval_time'
'_diffrn_standards.interval_time'
_definition.update 2012-11-26
_description.text
;
Time between the standard reflection measurements.
;
_name.category_id diffrn_standard
_name.object_id interval_time
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code minutes
save_
save__diffrn_standard.number
_definition.id '_diffrn_standard.number'
loop_
_alias.definition_id
'_diffrn_standard.number'
'_diffrn_standards_number'
'_diffrn_standards.number'
_definition.update 2012-11-26
_description.text
;
Number of unique standard reflections used in measurements.
;
_name.category_id diffrn_standard
_name.object_id number
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save__diffrn_standard.scale_su_average
_definition.id '_diffrn_standard.scale_su_average'
loop_
_alias.definition_id
'_diffrn_standard.scale_su_average'
'_diffrn_standards_scale_sigma'
'_diffrn_standards.scale_sigma'
'_diffrn_standards.scale_u'
'_diffrn_standards_scale_u'
_definition.update 2013-01-20
_description.text
;
The average standard uncertainty of the individual standard scales
applied to the intensity data.
;
_name.category_id diffrn_standard
_name.object_id scale_su_average
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save_DIFFRN_STANDARD_REFLN
_definition.id DIFFRN_STANDARD_REFLN
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items which specify the "standard" reflections
measured repeatedly to monitor variations in intensity due to source
flux, environment conditions or crystal quality.
;
_name.category_id DIFFRN_STANDARD
_name.object_id DIFFRN_STANDARD_REFLN
_category.key_id '_diffrn_standard_refln.key'
_category.key_list ['_diffrn_standard_refln.index_h'
'_diffrn_standard_refln.index_k'
'_diffrn_standard_refln.index_l']
save_
save__diffrn_standard_refln.code
_definition.id '_diffrn_standard_refln.code'
loop_
_alias.definition_id
'_diffrn_standard_refln.code'
'_diffrn_standard_refln_code'
'_diffrn_standard_refln.diffrn_id'
_definition.update 2012-11-26
_description.text
;
Code identifying a standard reflection used to monitor source
intensity variations or crystal degradation or movement during
data collection.
;
_name.category_id diffrn_standard_refln
_name.object_id code
_name.linked_item_id '_diffrn_refln.standard_code'
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_description_example.case
s1
save_
save__diffrn_standard_refln.hkl
_definition.id '_diffrn_standard_refln.hkl'
loop_
_alias.definition_id
'_diffrn_standard_refln.hkl'
_definition.update 2012-11-26
_description.text
;
Miller indices of a standard reflection.
;
_name.category_id diffrn_standard_refln
_name.object_id hkl
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Integer
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With d as diffrn_standard_refln
_diffrn_standard_refln.hkl = [d.index_h, d.index_h, d.index_l]
;
save_
save__diffrn_standard_refln.index_h
_definition.id '_diffrn_standard_refln.index_h'
loop_
_alias.definition_id
'_diffrn_standard_refln.index_h'
'_diffrn_standard_refln_index_h'
_name.category_id diffrn_standard_refln
_name.object_id index_h
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__diffrn_standard_refln.index_k
_definition.id '_diffrn_standard_refln.index_k'
loop_
_alias.definition_id
'_diffrn_standard_refln.index_k'
'_diffrn_standard_refln_index_k'
_name.category_id diffrn_standard_refln
_name.object_id index_k
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__diffrn_standard_refln.index_l
_definition.id '_diffrn_standard_refln.index_l'
loop_
_alias.definition_id
'_diffrn_standard_refln.index_l'
'_diffrn_standard_refln_index_l'
_name.category_id diffrn_standard_refln
_name.object_id index_l
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__diffrn_standard_refln.key
_definition.id '_diffrn_standard_refln.key'
loop_
_alias.definition_id
'_diffrn_standard_refln.key'
_definition.update 2012-11-26
_description.text
;
Value is a unique key to a set of DIFFRN_STANDARD_REFLN items
in a looped list.
;
_name.category_id diffrn_standard_refln
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Definition ' _type.contents = Type_Contents(diffrn_standard_refln.code)'
Evaluation ' _diffrn_standard_refln.key = _diffrn_standard_refln.code'
save_
save_REFLN
_definition.id REFLN
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to describe the reflection data
used in the refinement of a crystallographic structure model.
;
_name.category_id DIFFRACTION
_name.object_id REFLN
_category.key_id '_refln.key'
_category.key_list ['_refln.index_h' '_refln.index_k' '_refln.index_l']
save_
save__refln.A_calc
_definition.id '_refln.A_calc'
loop_
_alias.definition_id
'_refln.A_calc'
'_refln_A_calc'
_definition.update 2012-11-26
_description.text
;
The calculated real structure-factor component A =|Fcalc|cos(phase)
;
_name.category_id refln
_name.object_id A_calc
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.default 0.
loop_
_method.purpose
_method.expression
Definition
;
If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres"
Else If (_diffrn_radiation.probe == "electron") _units.code = "volts"
Else _units.code = "electrons"
;
Evaluation
;
_refln.A_calc = Real ( _refln.F_complex )
;
save_
save__refln.A_meas
_definition.id '_refln.A_meas'
loop_
_alias.definition_id
'_refln.A_meas'
'_refln_A_meas'
_definition.update 2012-11-26
_description.text
;
The measured real structure-factor component A =|Fmeas|cos(phase)
;
_name.category_id refln
_name.object_id A_meas
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.default 0.
loop_
_method.purpose
_method.expression
Definition
;
If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres"
Else If (_diffrn_radiation.probe == "electron") _units.code = "volts"
Else _units.code = "electrons"
;
save_
save__refln.B_calc
_definition.id '_refln.B_calc'
loop_
_alias.definition_id
'_refln.B_calc'
'_refln_B_calc'
_definition.update 2012-11-26
_description.text
;
The calculated imaginary structure-factor component B =|Fcalc|sin(phase)
;
_name.category_id refln
_name.object_id B_calc
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.default 0.
loop_
_method.purpose
_method.expression
Definition
;
If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres"
Else If (_diffrn_radiation.probe == "electron") _units.code = "volts"
Else _units.code = "electrons"
;
Evaluation
;
_refln.B_calc = Imag ( _refln.F_complex )
;
save_
save__refln.B_meas
_definition.id '_refln.B_meas'
loop_
_alias.definition_id
'_refln.B_meas'
'_refln_B_meas'
_definition.update 2012-11-26
_description.text
;
The measured imaginary structure-factor component B =|Fmeas|sin(phase)
;
_name.category_id refln
_name.object_id B_meas
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.default 0.
loop_
_method.purpose
_method.expression
Definition
;
If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres"
Else If (_diffrn_radiation.probe == "electron") _units.code = "volts"
Else _units.code = "electrons"
;
save_
save__refln.class_code
_definition.id '_refln.class_code'
loop_
_alias.definition_id
'_refln.class_code'
'_refln_class_code'
_definition.update 2012-11-26
_description.text
;
Code identifying the class to which this reflection has been
assigned. This code must match a value of _reflns_class.code.
Reflections may be grouped into classes for a variety of
purposes. For example, for modulated structures each reflection
class may be defined by the number m=sum|m~i~|, where the m~i~
are the integer coefficients that, in addition to h,k,l, index
the corresponding diffraction vector in the basis defined
for the reciprocal lattice.
;
_name.category_id refln
_name.object_id class_code
_name.linked_item_id '_reflns_class.code'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save__refln.crystal_id
_definition.id '_refln.crystal_id'
loop_
_alias.definition_id
'_refln.crystal_id'
'_refln_crystal_id'
_definition.update 2012-11-26
_description.text
;
Code identifying each crystal if multiple crystals are used. Is
used to link with crystals identified by _exptl_crystal.id.
;
_name.category_id refln
_name.object_id crystal_id
_name.linked_item_id '_exptl_crystal.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save__refln.d_spacing
_definition.id '_refln.d_spacing'
loop_
_alias.definition_id
'_refln.d_spacing'
'_refln_d_spacing'
_definition.update 2012-11-26
_description.text
;
The distance in angstroms between lattice planes in the crystal
with the indices _refln.hkl for this reflection.
;
_name.category_id refln
_name.object_id d_spacing
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
loop_
_method.purpose
_method.expression
Evaluation
;
_refln.d_spacing = 2. / _refln.sin_theta_over_lambda
;
save_
save__refln.F_calc
_definition.id '_refln.F_calc'
loop_
_alias.definition_id
'_refln.F_calc'
'_refln_F_calc'
_definition.update 2013-02-21
_description.text
;
The structure factor amplitude for the reflection calculated from
the atom site data.
;
_name.category_id refln
_name.object_id F_calc
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.default 0.
loop_
_method.purpose
_method.expression
Definition
;
If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres"
Else If (_diffrn_radiation.probe == "electron") _units.code = "volts"
Else _units.code = "electrons"
;
Evaluation
;
_refln.F_calc = Magn ( _refln.F_complex )
;
save_
save__refln.F_complex
_definition.id '_refln.F_complex'
loop_
_alias.definition_id
'_refln.F_complex'
'_refln_F_complex'
_definition.update 2013-04-23
_description.text
;
The structure factor vector for the reflection calculated from
the atom site data.
;
_name.category_id refln
_name.object_id F_complex
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Complex
_enumeration.default 0.
loop_
_method.purpose
_method.expression
Definition
;
If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres"
Else If (_diffrn_radiation.probe == "electron") _units.code = "volts"
Else _units.code = "electrons"
;
Evaluation
;
With r as refln
fc = Complex (0., 0.)
h = r.hkl
Loop a as atom_site {
f = a.site_symmetry_multiplicity * a.occupancy * (
r.form_factor_table [a.type_symbol] +
_atom_type_scat[a.type_symbol].dispersion )
Loop s as symmetry_equiv {
t = Exp(-h * s.R * a.tensor_beta * s.RT * h)
fc += f * t * ExpImag(TwoPi *( h *( s.R * a.fract_xyz + s.T)))
} }
_refln.F_complex = fc / _symmetry.multiplicity
;
save_
save__refln.F_meas
_definition.id '_refln.F_meas'
loop_
_alias.definition_id
'_refln.F_meas'
'_refln_F_meas'
_definition.update 2013-02-21
_description.text
;
The structure factor amplitude for the reflection derived from the
measured intensities.
;
_name.category_id refln
_name.object_id F_meas
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.default 0.
loop_
_method.purpose
_method.expression
Definition
;
If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres"
Else If (_diffrn_radiation.probe == "electron") _units.code = "volts"
Else _units.code = "electrons"
;
save_
save__refln.F_meas_su
_definition.id '_refln.F_meas_su'
loop_
_alias.definition_id
'_refln.F_meas_su'
'_refln_F_sigma'
'_refln.F_meas_sigma'
'_refln_F_meas_su'
_definition.update 2013-02-21
_description.text
;
The standard uncertainty of the measured structure factor amplitude.
;
_name.category_id refln
_name.object_id F_meas_su
_name.linked_item_id '_refln.F_meas'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.default 0.
loop_
_method.purpose
_method.expression
Definition
;
If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres"
Else If (_diffrn_radiation.probe == "electron") _units.code = "volts"
Else _units.code = "electrons"
;
save_
save__refln.F_squared_calc
_definition.id '_refln.F_squared_calc'
loop_
_alias.definition_id
'_refln.F_squared_calc'
'_refln_F_squared_calc'
_definition.update 2012-11-26
_description.text
;
The structure factor amplitude squared for the reflection calculated from
the atom site data.
;
_name.category_id refln
_name.object_id F_squared_calc
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.default 0.
loop_
_method.purpose
_method.expression
Definition
;
If (_diffrn_radiation.probe == "neutron")
_units.code = "femtometre_squared"
Else If (_diffrn_radiation.probe == "electron")
_units.code = "volt_squared"
Else _units.code = "electron_squared"
;
save_
save__refln.F_squared_meas
_definition.id '_refln.F_squared_meas'
loop_
_alias.definition_id
'_refln.F_squared_meas'
'_refln_F_squared_meas'
_definition.update 2013-02-21
_description.text
;
The structure factor amplitude for the reflection derived from the
measured intensities.
;
_name.category_id refln
_name.object_id F_squared_meas
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.default 0.
loop_
_method.purpose
_method.expression
Definition
;
If (_diffrn_radiation.probe == "neutron")
_units.code = "femtometre_squared"
Else If (_diffrn_radiation.probe == "electron")
_units.code = "volt_squared"
Else _units.code = "electron_squared"
;
save_
save__refln.F_squared_meas_su
_definition.id '_refln.F_squared_meas_su'
loop_
_alias.definition_id
'_refln.F_squared_meas_su'
'_refln_F_squared_sigma'
'_refln.F_squared_sigma'
'_refln_F_squared_meas_su'
_definition.update 2012-11-26
_description.text
;
The standard uncertainty of the measured structure factor squared.
;
_name.category_id refln
_name.object_id F_squared_meas_su
_name.linked_item_id '_refln.F_squared_meas'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.default 0.
loop_
_method.purpose
_method.expression
Definition
;
If (_diffrn_radiation.probe == "neutron")
_units.code = "femtometre_squared"
Else If (_diffrn_radiation.probe == "electron")
_units.code = "volt_squared"
Else _units.code = "electron_squared"
;
save_
save__refln.fom
_definition.id '_refln.fom'
loop_
_alias.definition_id
'_refln.fom'
_definition.update 2014-06-12
_description.text
;
The figure of merit m for this reflection.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that the phase angle a is correct
int is taken over the range alpha = 0 to 2 pi.
;
_name.category_id refln
_name.object_id fom
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
save_
save__refln.form_factor_table
_definition.id '_refln.form_factor_table'
loop_
_alias.definition_id
'_refln.form_factor_table'
_definition.update 2013-04-23
_description.text
;
Atomic scattering factor table for the scattering angle
of this diffraction vector and atom types in structure.
;
_name.category_id refln
_name.object_id form_factor_table
_type.purpose Number
_type.source Derived
_type.container Table
_type.contents Real
_type.dimension []
_units.code none
loop_
_method.purpose
_method.expression
Evaluation
;
With r as refln
table = Table ()
s = r.sin_theta_over_lambda
Loop t as atom_type {
If (_diffrn_radiation.probe == 'neutron') {
f = t.length_neutron
} Else If (s < 2.0 ) {
c = t.Cromer_Mann_coeffs
f = (c[0] + c[1] * Exp (-c[2] * s*s)
+ c[3] * Exp (-c[4] * s*s)
+ c[5] * Exp (-c[6] * s*s)
+ c[7] * Exp (-c[8] * s*s))
} Else {
c = t.hi_ang_Fox_coeffs
f = Exp ( c[0] + c[1]*s + c[2]*s*s + c[3]*s*s*s )
}
table [ t.symbol ] = f
}
_refln.form_factor_table = table
;
save_
save__refln.hkl
_definition.id '_refln.hkl'
loop_
_alias.definition_id
'_refln.hkl'
_definition.update 2012-11-26
_description.text
;
The Miller indices as a reciprocal space vector.
;
_name.category_id refln
_name.object_id hkl
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Integer
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With r as refln
_refln.hkl = [r.index_h, r.index_k, r.index_l]
;
save_
save__refln.include_status
_definition.id '_refln.include_status'
loop_
_alias.definition_id
'_refln.include_status'
'_refln_include_status'
'_refln_observed_status'
'_refln.observed_status'
'_refln.status'
_definition.update 2013-03-07
_description.text
;
Code indicating how the reflection was included in the refinement
and R-factor calculations.
;
_name.category_id refln
_name.object_id include_status
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
o 'ob : within _reflns.threshold_expression; within d-res limits'
< 'lt : without _reflns.threshold_expression; within d-res limits'
- 'sa : systematically absent reflection due to symmetry'
x 'du : deemed unreliable measurement -- not used'
h 'hd : above _refine_ls.d_res_high'
l 'ld : below _refine_ls.d_res_low'
_enumeration.default o
save_
save__refln.index_h
_definition.id '_refln.index_h'
loop_
_alias.definition_id
'_refln.index_h'
'_refln_index_h'
_name.category_id refln
_name.object_id index_h
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__refln.index_k
_definition.id '_refln.index_k'
loop_
_alias.definition_id
'_refln.index_k'
'_refln_index_k'
_name.category_id refln
_name.object_id index_k
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__refln.index_l
_definition.id '_refln.index_l'
loop_
_alias.definition_id
'_refln.index_l'
'_refln_index_l'
_name.category_id refln
_name.object_id index_l
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__refln.intensity_calc
_definition.id '_refln.intensity_calc'
loop_
_alias.definition_id
'_refln.intensity_calc'
'_refln_intensity_calc'
_definition.update 2012-11-26
_description.text
;
The intensity of the reflection calculated from the atom site data.
;
_name.category_id refln
_name.object_id intensity_calc
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code none
loop_
_method.purpose
_method.expression
Evaluation
;
_refln.intensity_calc = _refln.F_squared_calc / _refln.Lp_factor
;
save_
save__refln.intensity_meas
_definition.id '_refln.intensity_meas'
loop_
_alias.definition_id
'_refln.intensity_meas'
'_refln_intensity_meas'
_definition.update 2013-04-11
_description.text
;
The intensity of the reflection derived from the diffraction measurements.
;
_name.category_id refln
_name.object_id intensity_meas
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code none
save_
save__refln.intensity_meas_su
_definition.id '_refln.intensity_meas_su'
loop_
_alias.definition_id
'_refln.intensity_meas_su'
'_refln_intensity_meas_su'
'_refln.intensity_sigma'
'_refln_intensity_sigma'
_definition.update 2013-01-23
_description.text
;
standard uncertainty of the measured intensity.
;
_name.category_id refln
_name.object_id intensity_meas_su
_name.linked_item_id '_refln.intensity_meas'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code none
save_
save__refln.key
_definition.id '_refln.key'
loop_
_alias.definition_id
'_refln.key'
_definition.update 2012-11-26
_description.text
;
Value is a unique key to a set of REFLN items
in a looped list.
;
_name.category_id refln
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Matrix
_type.contents Integer
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation ' _refln.key = _refln.hkl'
save_
save__refln.Lp_factor
_definition.id '_refln.Lp_factor'
loop_
_alias.definition_id
'_refln.Lp_factor'
'_refln_Lp_factor'
_definition.update 2012-11-26
_description.text
;
The Lorentz-polarization factor appropriate for the instrument
used to measure the diffraction intensity. This is applied to
convert the net intensity into the measured F squared.
;
_name.category_id refln
_name.object_id Lp_factor
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code none
save_
save__refln.mean_path_length_tbar
_definition.id '_refln.mean_path_length_tbar'
loop_
_alias.definition_id
'_refln.mean_path_length_tbar'
'_refln_mean_path_length_tbar'
_definition.update 2012-11-26
_description.text
;
Mean path length through the crystal for this diffraction vector.
;
_name.category_id refln
_name.object_id mean_path_length_tbar
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code millimetres
save_
save__refln.phase_calc
_definition.id '_refln.phase_calc'
loop_
_alias.definition_id
'_refln.phase_calc'
'_refln_phase_calc'
_definition.update 2013-04-27
_description.text
;
The phase of the calculated structure-factor.
;
_name.category_id refln
_name.object_id phase_calc
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:360.
_units.code degrees
loop_
_method.purpose
_method.expression
Evaluation
;
phase = Atan2d ( _refln.B_calc, _refln.A_calc )
If(phase < 0.) _refln.phase_calc = phase + 360.
Else _refln.phase_calc = phase
;
save_
save__refln.phase_meas
_definition.id '_refln.phase_meas'
loop_
_alias.definition_id
'_refln.phase_meas'
'_refln_phase_meas'
_definition.update 2012-11-26
_description.text
;
The phase of the measured structure-factor. This may be derived from
the atom site data if available or from the phase solution process
prior to determination of the structure.
;
_name.category_id refln
_name.object_id phase_meas
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:360.
_units.code degrees
save_
save__refln.refinement_status
_definition.id '_refln.refinement_status'
loop_
_alias.definition_id
'_refln.refinement_status'
'_refln_refinement_status'
_definition.update 2012-11-26
_description.text
;
Status code of reflection in the structure refinement process.
;
_name.category_id refln
_name.object_id refinement_status
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
incl 'included in ls process'
excl 'excluded from ls process'
extn 'excluded due to extinction'
_enumeration.default incl
save_
save__refln.scale_group_code
_definition.id '_refln.scale_group_code'
loop_
_alias.definition_id
'_refln.scale_group_code'
'_refln_scale_group_code'
_definition.update 2012-11-26
_description.text
;
Code identifying the scale (if there is more than one scale) used
convert the measured structure factor to a common absolute value.
;
_name.category_id refln
_name.object_id scale_group_code
_name.linked_item_id '_reflns_scale.group_code'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save__refln.sin_theta_over_lambda
_definition.id '_refln.sin_theta_over_lambda'
loop_
_alias.definition_id
'_refln.sin_theta_over_lambda'
'_refln_sint/lambda'
'_refln_sin_theta_over_lambda'
'_refln.sint_over_lambda'
_definition.update 2013-03-07
_description.text
;
The (sin theta)/lambda value for this reflection.
;
_name.category_id refln
_name.object_id sin_theta_over_lambda
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code reciprocal_angstroms
loop_
_method.purpose
_method.expression
Evaluation
;
With r as refln
h = r.hkl
G = _cell_reciprocal.metric_tensor
r.sin_theta_over_lambda = Sqrt ( h * G * h ) / 2.
;
save_
save__refln.symmetry_epsilon
_definition.id '_refln.symmetry_epsilon'
loop_
_alias.definition_id
'_refln.symmetry_epsilon'
'_refln_symmetry_epsilon'
_definition.update 2012-11-26
_description.text
;
The symmetry reinforcement factor corresponding to the number of
times the reflection indices are generated identically from the
space-group symmetry operations.
;
_name.category_id refln
_name.object_id symmetry_epsilon
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Index
_enumeration.range 1:48
save_
save__refln.symmetry_multiplicity
_definition.id '_refln.symmetry_multiplicity'
loop_
_alias.definition_id
'_refln.symmetry_multiplicity'
'_refln_symmetry_multiplicity'
_definition.update 2012-11-26
_description.text
;
The number of reflections symmetry-equivalent under the Laue
symmetry to the present reflection. In the Laue symmetry, Friedel
opposites (h k l and -h -k -l) are equivalent. Tables of
symmetry-equivalent reflections are available in International
Tables for Crystallography, Volume A (1987), section 10.2.
;
_name.category_id refln
_name.object_id symmetry_multiplicity
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Index
_enumeration.range 1:48
save_
save__refln.wavelength
_definition.id '_refln.wavelength'
loop_
_alias.definition_id
'_refln.wavelength'
'_refln_wavelength'
_definition.update 2012-11-26
_description.text
;
The mean wavelength in angstroms of radiation used to measure
this reflection. This is an important parameter for data
collected using energy-dispersive detectors or the Laue method.
;
_name.category_id refln
_name.object_id wavelength
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__refln.wavelength_id
_definition.id '_refln.wavelength_id'
loop_
_alias.definition_id
'_refln.wavelength_id'
'_refln_wavelength_id'
_definition.update 2012-11-26
_description.text
;
Code identifying the wavelength in DIFFRN_RADIATION_WAVELENGTH list.
;
_name.category_id refln
_name.object_id wavelength_id
_name.linked_item_id '_diffrn_radiation_wavelength.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save_REFLNS
_definition.id REFLNS
_definition.scope Category
_definition.class Set
_definition.update 2012-11-26
_description.text
;
The CATEGORY of data items used to specify parameters for the complete
set of reflections used in the structure refinement process. Note that
these parameters are often similar measures to those defined in the
DIFFRN categories, but differ in that the parameters refer to the
reduced/transformed reflections which have been used to refine the
atom site data in the ATOM_SITE category. The DIFFRN definitions refer
to the diffraction measurements and the raw reflection data.
;
_name.category_id DIFFRACTION
_name.object_id REFLNS
save_
save__reflns.apply_dispersion_to_Fcalc
_definition.id '_reflns.apply_dispersion_to_Fcalc'
loop_
_alias.definition_id
'_reflns.apply_dispersion_to_Fcalc'
_definition.update 2013-04-28
_description.text
;
Yes or No flag on whether the anomalous dispersion scattering
components will be applied in the F_complex calculation.
See _refln.F_complex
;
_name.category_id reflns
_name.object_id apply_dispersion_to_Fcalc
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
Yes 'Apply dispersion'
No 'Do not apply dispersion'
_enumeration.default Yes
save_
save__reflns.d_resolution_high
_definition.id '_reflns.d_resolution_high'
loop_
_alias.definition_id
'_reflns.d_resolution_high'
'_reflns_d_resolution_high'
_definition.update 2012-11-26
_description.text
;
Highest resolution for the final REFLN data set.
This corresponds to the smallest interpanar d value.
;
_name.category_id reflns
_name.object_id d_resolution_high
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__reflns.d_resolution_low
_definition.id '_reflns.d_resolution_low'
loop_
_alias.definition_id
'_reflns.d_resolution_low'
'_reflns_d_resolution_low'
_definition.update 2012-11-26
_description.text
;
Lowest resolution for the final REFLN data set.
This corresponds to the largest interpanar d value.
;
_name.category_id reflns
_name.object_id d_resolution_low
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__reflns.Friedel_coverage
_definition.id '_reflns.Friedel_coverage'
loop_
_alias.definition_id
'_reflns.Friedel_coverage'
'_reflns_Friedel_coverage'
_definition.update 2012-11-26
_description.text
;
The proportion of Friedel related reflections present in the number of
the 'independent reflections' specified by the item _reflns.number_total.
This proportion is calculated as the ratio:
[N(Crystal class) - N(Laue symmetry)] / N(Laue symmetry)
where, working from the @diffrn_refln_ list,
N(Crystal class) is the number of reflections obtained on
averaging under the symmetry of the crystal class
N(Laue symmetry) is the number of reflections obtained on
averaging under the Laue symmetry.
(a) For centrosymmetric structures its value is
necessarily equal to 0.0 as the crystal class
is identical to the Laue symmetry.
(b) For whole-sphere data for a crystal in the space
group P1, _reflns.Friedel_coverage is equal to 1.0,
as no reflection h k l is equivalent to -h -k -l
in the crystal class and all Friedel pairs
{h k l; -h -k -l} have been measured.
(c) For whole-sphere data in space group Pmm2, the value
will be < 1.0 because although reflections h k l and
-h -k -l are not equivalent when h k l indices are
non-zero, they are when l=0.
(d) For a crystal in the group Pmm2 measurements of the
two inequivalent octants h >= 0, k >=0, l lead to the
same value as in (c), whereas measurements of the
two equivalent octants h >= 0, k, l >= 0 will lead to
a zero value for @reflns_Friedel_coverage.
;
_name.category_id reflns
_name.object_id Friedel_coverage
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save__reflns.Friedel_fraction_full
_definition.id '_reflns.Friedel_fraction_full'
loop_
_alias.definition_id
'_reflns.Friedel_fraction_full'
'_reflns_Friedel_fraction_full'
_definition.update 2013-01-20
_description.text
;
The ratio of Friedel pairs measured to _diffrn_reflns.theta_full
to the number theoretically possible (ignoring reflections in
centric projections and systematic absences throughout).
In contrast to _reflns.Friedel_coverage this can take values in
the full range 0 to 1 for any non-centrosymmetric space group,
and so one can see at a glance how completely the Friedel pairs
have been measured. For centrosymmetric space groups the value
would be given as not-applicable '.'
;
_name.category_id reflns
_name.object_id Friedel_fraction_full
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save__reflns.Friedel_fraction_max
_definition.id '_reflns.Friedel_fraction_max'
loop_
_alias.definition_id
'_reflns.Friedel_fraction_max'
'_reflns_Friedel_fraction_max'
_definition.update 2013-01-20
_description.text
;
The ratio of Friedel pairs measured to _diffrn_reflns.theta_max
to the number theoretically possible (ignoring reflections in
centric projections and systematic absences throughout).
In contrast to _reflns.Friedel_coverage this can take values in
the full range 0 to 1 for any non-centrosymmetric space group,
and so one can see at a glance how completely the Friedel pairs
have been measured. For centrosymmetric space groups the value
would be given as not-applicable '.'
;
_name.category_id reflns
_name.object_id Friedel_fraction_max
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save__reflns.limit_h_max
_definition.id '_reflns.limit_h_max'
loop_
_alias.definition_id
'_reflns.limit_h_max'
'_reflns_limit_h_max'
_name.category_id reflns
_name.object_id limit_h_max
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__reflns.limit_h_min
_definition.id '_reflns.limit_h_min'
loop_
_alias.definition_id
'_reflns.limit_h_min'
'_reflns_limit_h_min'
_name.category_id reflns
_name.object_id limit_h_min
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__reflns.limit_k_max
_definition.id '_reflns.limit_k_max'
loop_
_alias.definition_id
'_reflns.limit_k_max'
'_reflns_limit_k_max'
_name.category_id reflns
_name.object_id limit_k_max
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__reflns.limit_k_min
_definition.id '_reflns.limit_k_min'
loop_
_alias.definition_id
'_reflns.limit_k_min'
'_reflns_limit_k_min'
_name.category_id reflns
_name.object_id limit_k_min
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__reflns.limit_l_max
_definition.id '_reflns.limit_l_max'
loop_
_alias.definition_id
'_reflns.limit_l_max'
'_reflns_limit_l_max'
_name.category_id reflns
_name.object_id limit_l_max
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__reflns.limit_l_min
_definition.id '_reflns.limit_l_min'
loop_
_alias.definition_id
'_reflns.limit_l_min'
'_reflns_limit_l_min'
_name.category_id reflns
_name.object_id limit_l_min
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__reflns.limit_max
_definition.id '_reflns.limit_max'
loop_
_alias.definition_id
'_reflns.limit_max'
_definition.update 2013-01-15
_description.text
;
Maximum Miller indices of refined diffraction reflections.
;
_name.category_id reflns
_name.object_id limit_max
_type.purpose Number
_type.source Assigned
_type.container Matrix
_type.contents Real
_type.dimension [3]
_units.code none
loop_
_method.purpose
_method.expression
Evaluation
;
With t as reflns
_reflns.limit_max = [t.limit_h_max,t.limit_k_max,t.limit_l_max]
;
save_
save__reflns.limit_min
_definition.id '_reflns.limit_min'
loop_
_alias.definition_id
'_reflns.limit_min'
_definition.update 2013-01-15
_description.text
;
Minimum Miller indices of refined diffraction reflections.
;
_name.category_id reflns
_name.object_id limit_min
_type.purpose Number
_type.source Assigned
_type.container Matrix
_type.contents Real
_units.code none
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With t as reflns
_reflns.limit_min = [t.limit_h_min,t.limit_k_min,t.limit_l_min]
;
save_
save__reflns.number_gt
_definition.id '_reflns.number_gt'
loop_
_alias.definition_id
'_reflns.number_gt'
'_reflns_number_gt'
'_reflns_number_observed'
'_reflns_number_obs'
'_reflns.number_obs'
_definition.update 2012-11-26
_description.text
;
Count of reflections in the REFLN set (not the DIFFRN_REFLN set) which
are significantly intense (see _reflns.threshold_expression). It may
include Friedel equivalent reflections (i.e. those which are equivalent
under the Laue symmetry but inequivalent under the crystal class),
depending to the nature of the structure and the procedures used.
;
_name.category_id reflns
_name.object_id number_gt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save__reflns.number_total
_definition.id '_reflns.number_total'
loop_
_alias.definition_id
'_reflns.number_total'
'_reflns_number_total'
'_reflns_number_all'
'_reflns.number_all'
_definition.update 2012-11-26
_description.text
;
Number of reflections in the REFLN set (not the DIFFRN_REFLN set). It may
include Friedel equivalent reflections (i.e. those which are equivalent
under the Laue symmetry but inequivalent under the crystal class),
depending to the nature of the structure and the procedures used.
;
_name.category_id reflns
_name.object_id number_total
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save__reflns.special_details
_definition.id '_reflns.special_details'
loop_
_alias.definition_id
'_reflns.special_details'
'_reflns_special_details'
'_reflns.details'
_definition.update 2012-11-26
_description.text
;
Description of the properties of the REFLN reflection list that is not
given in other data items. Should include details about the averaging
of symmetry-equivalent reflections including Friedel pairs.
;
_name.category_id reflns
_name.object_id special_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__reflns.threshold_expression
_definition.id '_reflns.threshold_expression'
loop_
_alias.definition_id
'_reflns.threshold_expression'
'_reflns_threshold_expression'
'_reflns_observed_criterion'
'_reflns.observed_criterion'
_definition.update 2012-11-26
_description.text
;
Description of the criterion used to classify a reflection as having a
"significant intensity". This criterion is usually expressed in terms
of a u(I) or u(F) threshold. "u" is the standard uncertainty.
;
_name.category_id reflns
_name.object_id threshold_expression
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
I>2u(I)
save_
save_REFLNS_CLASS
_definition.id REFLNS_CLASS
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items which specify the properties of reflections
in specific classes of reflections.
;
_name.category_id REFLNS
_name.object_id REFLNS_CLASS
_category.key_id '_reflns_class.key'
_category.key_list ['_reflns_class.code']
save_
save__reflns_class.code
_definition.id '_reflns_class.code'
loop_
_alias.definition_id
'_reflns_class.code'
'_reflns_class_code'
_definition.update 2012-11-26
_description.text
;
Code identifying a reflection class.
;
_name.category_id reflns_class
_name.object_id code
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_description_example.case
c1
save_
save__reflns_class.d_res_high
_definition.id '_reflns_class.d_res_high'
loop_
_alias.definition_id
'_reflns_class.d_res_high'
'_reflns_class_d_res_high'
_definition.update 2012-11-26
_description.text
;
Highest resolution for the reflections in this class.
This corresponds to the smallest interpanar d value.
;
_name.category_id reflns_class
_name.object_id d_res_high
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__reflns_class.d_res_low
_definition.id '_reflns_class.d_res_low'
loop_
_alias.definition_id
'_reflns_class.d_res_low'
'_reflns_class_d_res_low'
_definition.update 2012-11-26
_description.text
;
Lowest resolution for the reflections in this class.
This corresponds to the largest interpanar d value.
;
_name.category_id reflns_class
_name.object_id d_res_low
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__reflns_class.description
_definition.id '_reflns_class.description'
loop_
_alias.definition_id
'_reflns_class.description'
'_reflns_class_description'
_definition.update 2012-11-26
_description.text
;
Description of a reflection class.
;
_name.category_id reflns_class
_name.object_id description
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'H0L0 common projection reflections'
save_
save__reflns_class.key
_definition.id '_reflns_class.key'
loop_
_alias.definition_id
'_reflns_class.key'
_definition.update 2012-11-26
_description.text
;
Value is a unique key to a set of REFLNS_CLASS items
in a looped list.
;
_name.category_id reflns_class
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _reflns_class.key = _reflns_class.code'
save_
save__reflns_class.number_gt
_definition.id '_reflns_class.number_gt'
loop_
_alias.definition_id
'_reflns_class.number_gt'
'_reflns_class_number_observed'
'_reflns_class_number_gt'
_definition.update 2012-11-26
_description.text
;
Count of reflections in this REFLN class (not the DIFFRN_REFLN set)
which are significantly intense (see _reflns.threshold_expression). It may
include Friedel equivalent reflections (i.e. those which are equivalent
under the Laue symmetry but inequivalent under the crystal class),
depending to the nature of the structure and the procedures used.
;
_name.category_id reflns_class
_name.object_id number_gt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save__reflns_class.number_total
_definition.id '_reflns_class.number_total'
loop_
_alias.definition_id
'_reflns_class.number_total'
'_reflns_class_number_total'
_definition.update 2012-11-26
_description.text
;
Count of reflections in this REFLN class (not the DIFFRN_REFLN set). It
may include Friedel equivalent reflections (those which are equivalent
under the Laue symmetry but inequivalent under the crystal class),
depending to the nature of the structure and the procedures used.
;
_name.category_id reflns_class
_name.object_id number_total
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save__reflns_class.R_factor_all
_definition.id '_reflns_class.R_factor_all'
loop_
_alias.definition_id
'_reflns_class.R_factor_all'
'_reflns_class_R_factor_all'
_definition.update 2012-11-26
_description.text
;
Residual factor for reflections in this class used in refinement.
sum | F(meas) - F(calc) |
R(F all) = ------------------------
sum | F(meas) |
F(meas) = the measured structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the specified reflections
;
_name.category_id reflns_class
_name.object_id R_factor_all
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__reflns_class.R_factor_gt
_definition.id '_reflns_class.R_factor_gt'
loop_
_alias.definition_id
'_reflns_class.R_factor_gt'
'_reflns_class_R_factor_gt'
'_reflns_class_R_factor_observed'
_definition.update 2012-11-26
_description.text
;
Residual factor for the reflections in this class judged
significantly intense (i.e. greater than required by the
_reflns.threshold_expression) and included in the refinement.
sum | F(meas_gt) - F(calc) |
R(F gt) = --------------------------------
sum | F(meas_gt) |
F(meas) = the measured structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the specified reflections
;
_name.category_id reflns_class
_name.object_id R_factor_gt
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__reflns_class.R_Fsqd_factor
_definition.id '_reflns_class.R_Fsqd_factor'
loop_
_alias.definition_id
'_reflns_class.R_Fsqd_factor'
'_reflns_class_R_Fsqd_factor'
_definition.update 2012-11-26
_description.text
;
Residual factor R(F^2^) for reflections in this class judged
significantly intense (i.e. greater than required by the
_reflns.threshold_expression) and included in the refinement.
sum | F(meas_gt)^2^ - F(calc)^2^ |
R(Fsqd gt) = ------------------------------------
sum F(meas_gt)^2^
F(meas_gt)^2^ = square of the 'observed' structure-factor
F(calc )^2^ = square of the calculated structure-factor
and the sum is taken over the specified reflections
;
_name.category_id reflns_class
_name.object_id R_Fsqd_factor
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__reflns_class.R_I_factor
_definition.id '_reflns_class.R_I_factor'
loop_
_alias.definition_id
'_reflns_class.R_I_factor'
'_reflns_class_R_I_factor'
_definition.update 2012-11-26
_description.text
;
Residual factor R(I) for reflections in this class judged
significantly intense (i.e. greater than required by the
_reflns.threshold_expression) and included in the refinement.
sum | I(meas_gt) - I(calc) |
R(I gt) = ----------------------------
sum | I(meas_gt) |
I(meas_gt) = the net 'observed' intensity
I(calc ) = the net calculated intensity
and the sum is taken over the specified reflections
;
_name.category_id reflns_class
_name.object_id R_I_factor
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__reflns_class.wR_factor_all
_definition.id '_reflns_class.wR_factor_all'
loop_
_alias.definition_id
'_reflns_class.wR_factor_all'
'_reflns_class_wR_factor_all'
_definition.update 2012-11-26
_description.text
;
For each reflection class, the weighted residual factors for all
reflections included in the refinement. The reflections also
satisfy the resolution limits established by
_reflns_class.d_res_high and _reflns_class.d_res_low.
( sum w [ Y(meas) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------- )
( sum w Y(meas)^2^ )
Y(meas) = the measured amplitudes specified by
_refine_ls.structure_factor_coef
Y(calc) = the calculated amplitudes specified by
_refine_ls.structure_factor_coef
w = the least-squares weights
and the sum is taken over the reflections of this class.
;
_name.category_id reflns_class
_name.object_id wR_factor_all
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save_REFLNS_SCALE
_definition.id REFLNS_SCALE
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items which specify the scales needed to place
measured structure factor coefficients on the same absolute scale.
;
_name.category_id REFLNS
_name.object_id REFLNS_SCALE
_category.key_id '_reflns_scale.key'
_category.key_list ['_reflns_scale.group_code']
save_
save__reflns_scale.group_code
_definition.id '_reflns_scale.group_code'
loop_
_alias.definition_id
'_reflns_scale.group_code'
'_reflns_scale_group_code'
_definition.update 2012-11-26
_description.text
;
Code identifying a reflection scale group. These names need not
correspond to _diffrn_scale_group.code names.
;
_name.category_id reflns_scale
_name.object_id group_code
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__reflns_scale.key
_definition.id '_reflns_scale.key'
loop_
_alias.definition_id
'_reflns_scale.key'
_definition.update 2012-11-26
_description.text
;
Value is a unique key to a set of REFLNS_SCALE items
in a looped list.
;
_name.category_id reflns_scale
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _reflns_scale.key = _reflns_scale.group_code'
save_
save__reflns_scale.meas_F
_definition.id '_reflns_scale.meas_F'
loop_
_alias.definition_id
'_reflns_scale.meas_F'
'_reflns_scale_meas_F'
_definition.update 2012-11-26
_description.text
;
Structure factor scale for this scale group.
;
_name.category_id reflns_scale
_name.object_id meas_F
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__reflns_scale.meas_F_squared
_definition.id '_reflns_scale.meas_F_squared'
loop_
_alias.definition_id
'_reflns_scale.meas_F_squared'
'_reflns_scale_meas_F_squared'
_definition.update 2012-11-26
_description.text
;
Structure factor squared scale for this scale group.
;
_name.category_id reflns_scale
_name.object_id meas_F_squared
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__reflns_scale.meas_intensity
_definition.id '_reflns_scale.meas_intensity'
loop_
_alias.definition_id
'_reflns_scale.meas_intensity'
'_reflns_scale_meas_intensity'
_definition.update 2012-11-26
_description.text
;
Net intensity scale for this scale group.
;
_name.category_id reflns_scale
_name.object_id meas_intensity
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save_REFLNS_SHELL
_definition.id REFLNS_SHELL
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items which specify the information about
reflections divided into shells bounded by d resolution limits.
;
_name.category_id REFLNS
_name.object_id REFLNS_SHELL
_category.key_id '_reflns_shell.key'
_category.key_list ['_reflns_shell.d_res_low' '_reflns_shell.d_res_high']
save_
save__reflns_shell.d_res_high
_definition.id '_reflns_shell.d_res_high'
loop_
_alias.definition_id
'_reflns_shell.d_res_high'
'_reflns_shell_d_res_high'
_definition.update 2012-11-26
_description.text
;
Highest resolution for the reflections in this shell.
This corresponds to the smallest interpanar d value.
;
_name.category_id reflns_shell
_name.object_id d_res_high
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__reflns_shell.d_res_limits
_definition.id '_reflns_shell.d_res_limits'
loop_
_alias.definition_id
'_reflns_shell.d_res_limits'
_definition.update 2012-11-26
_description.text
;
Resolution for the reflections in this shell stored as
the list of lowest and highest values. This is the
category key.
;
_name.category_id reflns_shell
_name.object_id d_res_limits
_type.purpose Number
_type.source Derived
_type.container List
_type.contents Real
_type.dimension [2]
_units.code angstroms
loop_
_method.purpose
_method.expression
Evaluation
;
With s as reflns_shell
_reflns_shell.d_res_limits = [ s.d_res_low, s.d_res_high ]
;
save_
save__reflns_shell.d_res_low
_definition.id '_reflns_shell.d_res_low'
loop_
_alias.definition_id
'_reflns_shell.d_res_low'
'_reflns_shell_d_res_low'
_definition.update 2012-11-26
_description.text
;
Lowest resolution for the reflections in this shell.
This corresponds to the largest interpanar d value.
;
_name.category_id reflns_shell
_name.object_id d_res_low
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__reflns_shell.key
_definition.id '_reflns_shell.key'
loop_
_alias.definition_id
'_reflns_shell.key'
_definition.update 2012-11-26
_description.text
;
Value is a unique key to a set of REFLNS_SHELL items
in a looped list.
;
_name.category_id reflns_shell
_name.object_id key
_type.purpose Key
_type.source Related
_type.container List
_type.contents Real
_type.dimension [2]
loop_
_method.purpose
_method.expression
Evaluation ' _reflns_shell.key = _reflns_shell.d_res_limits'
save_
save__reflns_shell.meanI_over_suI_all
_definition.id '_reflns_shell.meanI_over_suI_all'
loop_
_alias.definition_id
'_reflns_shell.meanI_over_suI_all'
'_reflns_shell_meanI_over_uI_all'
'_reflns_shell_meanI_over_sigI_all'
'_reflns_shell.meanI_over_sigI_all'
'_reflns_shell.meanI_over_uI_all'
_definition.update 2012-11-26
_description.text
;
Ratio of the mean intensity in a shell to the mean standard uncertainty
of the intensities in the shell.
;
_name.category_id reflns_shell
_name.object_id meanI_over_suI_all
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0:
_units.code none
save_
save__reflns_shell.meanI_over_suI_gt
_definition.id '_reflns_shell.meanI_over_suI_gt'
loop_
_alias.definition_id
'_reflns_shell.meanI_over_suI_gt'
'_reflns_shell_meanI_over_sigI_obs'
'_reflns_shell.meanI_over_sigI_obs'
'_reflns_shell.meanI_over_sigI_gt'
'_reflns_shell_meanI_over_sigI_gt'
'_reflns_shell.meanI_over_uI_gt'
'_reflns_shell_meanI_over_uI_gt'
_definition.update 2012-11-26
_description.text
;
Ratio of the mean intensity of significantly intense reflections (see
_reflns.threshold_expression) in this shell to the mean standard
uncertainty of the intensities in the shell.
;
_name.category_id reflns_shell
_name.object_id meanI_over_suI_gt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0:
_units.code none
save_
save__reflns_shell.number_measured_all
_definition.id '_reflns_shell.number_measured_all'
loop_
_alias.definition_id
'_reflns_shell.number_measured_all'
'_reflns_shell_number_measured_all'
_definition.update 2012-11-26
_description.text
;
Total count of reflections measured for this resolution shell.
;
_name.category_id reflns_shell
_name.object_id number_measured_all
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save__reflns_shell.number_measured_gt
_definition.id '_reflns_shell.number_measured_gt'
loop_
_alias.definition_id
'_reflns_shell.number_measured_gt'
'_reflns_shell_number_measured_obs'
'_reflns_shell.number_measured_obs'
'_reflns_shell_number_measured_gt'
_definition.update 2012-11-26
_description.text
;
Number of reflections measured for this resolution shell which are
significantly intense (see _reflns.threshold_expression).
;
_name.category_id reflns_shell
_name.object_id number_measured_gt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save__reflns_shell.number_possible
_definition.id '_reflns_shell.number_possible'
loop_
_alias.definition_id
'_reflns_shell.number_possible'
'_reflns_shell_number_possible'
'_reflns_shell.number_possible_all'
_definition.update 2012-11-26
_description.text
;
Count of symmetry-unique reflections possible in this reflection shell.
;
_name.category_id reflns_shell
_name.object_id number_possible
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save__reflns_shell.number_unique_all
_definition.id '_reflns_shell.number_unique_all'
loop_
_alias.definition_id
'_reflns_shell.number_unique_all'
'_reflns_shell_number_unique_all'
_definition.update 2012-11-26
_description.text
;
Count of symmetry-unique reflections present in this reflection shell.
;
_name.category_id reflns_shell
_name.object_id number_unique_all
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save__reflns_shell.number_unique_gt
_definition.id '_reflns_shell.number_unique_gt'
loop_
_alias.definition_id
'_reflns_shell.number_unique_gt'
'_reflns_shell_number_unique_gt'
'_reflns_shell_number_unique_obs'
'_reflns_shell.number_unique_obs'
_definition.update 2012-11-26
_description.text
;
Number of symmetry-unique reflections present in this reflection shell
which are significantly intense (see _reflns.threshold_expression).
;
_name.category_id reflns_shell
_name.object_id number_unique_gt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save__reflns_shell.percent_possible_all
_definition.id '_reflns_shell.percent_possible_all'
loop_
_alias.definition_id
'_reflns_shell.percent_possible_all'
'_reflns_shell_percent_possible_all'
_definition.update 2012-11-26
_description.text
;
Percentage of reflections present in this shell over that possible.
;
_name.category_id reflns_shell
_name.object_id percent_possible_all
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:100.0
_units.code none
save_
save__reflns_shell.percent_possible_gt
_definition.id '_reflns_shell.percent_possible_gt'
loop_
_alias.definition_id
'_reflns_shell.percent_possible_gt'
'_reflns_shell_percent_possible_gt'
'_reflns_shell_percent_possible_obs'
'_reflns_shell.percent_possible_obs'
_definition.update 2012-11-26
_description.text
;
Percentage of reflections present in this shell which are significantly
intense (see _reflns.threshold_expression), over that possible.
;
_name.category_id reflns_shell
_name.object_id percent_possible_gt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:100.0
_units.code none
save_
save__reflns_shell.Rmerge_F_all
_definition.id '_reflns_shell.Rmerge_F_all'
loop_
_alias.definition_id
'_reflns_shell.Rmerge_F_all'
'_reflns_shell_Rmerge_F_all'
_definition.update 2012-11-26
_description.text
;
Rmerge(F) for all reflections in a given shell.
sum~i~ ( sum~j~ | F~j~ - <F> | )
Rmerge(F) = --------------------------------
sum~i~ ( sum~j~ <F> )
F~j~ = the amplitude of the jth observation of reflection i
<F> = the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
_name.category_id reflns_shell
_name.object_id Rmerge_F_all
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__reflns_shell.Rmerge_F_gt
_definition.id '_reflns_shell.Rmerge_F_gt'
loop_
_alias.definition_id
'_reflns_shell.Rmerge_F_gt'
'_reflns_shell_Rmerge_F_obs'
'_reflns_shell.Rmerge_F_obs'
'_reflns_shell_Rmerge_F_gt'
_definition.update 2012-11-26
_description.text
;
Rmerge(F) for reflections in a shell which are significantly intense
(see _reflns.threshold_expression). The residual merge expression is
shown in the _reflns_shell.Rmerge_F_all definition.
;
_name.category_id reflns_shell
_name.object_id Rmerge_F_gt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__reflns_shell.Rmerge_I_all
_definition.id '_reflns_shell.Rmerge_I_all'
loop_
_alias.definition_id
'_reflns_shell.Rmerge_I_all'
'_reflns_shell_Rmerge_I_all'
_definition.update 2012-11-26
_description.text
;
Rmerge(I) for all reflections in a given shell.
sum~i~ ( sum~j~ | I~j~ - <I> | )
Rmerge(I) = --------------------------------
sum~i~ ( sum~j~ <I> )
I~j~ = the intensity of the jth observation of reflection i
<I> = the mean of the intensities of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
_name.category_id reflns_shell
_name.object_id Rmerge_I_all
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__reflns_shell.Rmerge_I_gt
_definition.id '_reflns_shell.Rmerge_I_gt'
loop_
_alias.definition_id
'_reflns_shell.Rmerge_I_gt'
'_reflns_shell_Rmerge_I_obs'
'_reflns_shell.Rmerge_I_obs'
'_reflns_shell_Rmerge_I_gt'
_definition.update 2012-11-26
_description.text
;
Rmerge(I) for reflections in a shell which are significantly intense
(see _reflns.threshold_expression). The residual merge expression is
shown in the _reflns_shell.Rmerge_I_all definition.
;
_name.category_id reflns_shell
_name.object_id Rmerge_I_gt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save_EXPERIMENTAL
_definition.id EXPERIMENTAL
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The DICTIONARY group encompassing the CORE experimental data defined
and used with in the Crystallographic Information Framework (CIF).
;
_name.category_id CIF_CORE
_name.object_id EXPERIMENTAL
save_
save_EXPERIMENTS
_definition.id EXPERIMENTS
_definition.scope Category
_definition.class Ref-loop
_definition.update 2013-09-08
_description.text
;
This category is designed specifically to facilitate studies
involving multiple sets of experiments and their associated data
values. The data items are defined within the EXPTL category.
This category class is only used in an instance document when
there is more than one experiment encompassed by the category
of EXPTL items. When this is the case each set of EXPTL data,
one set per experiment, is enclosed in its own save frame.
In the instance document these are referred to as a loop of
the item _experiments.key. See a typical example below.
When only one set of experimental data exists the EXPTL items
need not be enclosed in a save frame and the reference loop is
unnecessary.
;
_name.category_id EXPERIMENTAL
_name.object_id EXPERIMENTS
_category.key_id '_experiments.key'
_category.key_list ['_experiments.key']
loop_
_description_example.case
;
In an instance document this category is typically invoked as
loop_ _experiments.key
${"frame":"exptl_blue"}$
${"frame":"exptl_red"}$
;
save_
save__experiments.key
_definition.id '_experiments.key'
loop_
_alias.definition_id
'_experiments.key'
_definition.update 2012-11-22
_description.text
;
Unique key to a set of save frames in a looped list.
;
_name.category_id experiments
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Ref-table
_type.contents Name
loop_
_description_example.case
'${"frame":phase1}$'
save_
save_EXPTL
_definition.id EXPTL
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items used to specify the experimental work
prior to diffraction measurements. These include crystallization
crystal measurements and absorption-correction techniques used..
;
_name.category_id EXPERIMENTS
_name.object_id EXPTL
save_
save__exptl.crystals_number
_definition.id '_exptl.crystals_number'
loop_
_alias.definition_id
'_exptl.crystals_number'
'_exptl_crystals_number'
_definition.update 2012-11-22
_description.text
;
Total number of crystals used in the measurement of intensities.
;
_name.category_id exptl
_name.object_id crystals_number
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 1:
_enumeration.default 1
save_
save__exptl.id
_definition.id '_exptl.id'
loop_
_alias.definition_id
'_exptl.id'
_definition.update 2012-11-22
_description.text
;
Code identifying an experiment if there are multiple sets of
experimental data. See _experiments.key.
;
_name.category_id exptl
_name.object_id id
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__exptl.method
_definition.id '_exptl.method'
loop_
_alias.definition_id
'_exptl.method'
_definition.update 2014-06-12
_description.text
;
The method used in the experiment.
;
_name.category_id exptl
_name.object_id method
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'single-crystal x-ray diffraction'
'single-crystal neutron diffraction'
'single-crystal electron diffraction'
'fiber x-ray diffraction'
'fiber neutron diffraction'
'fiber electron diffraction'
'single-crystal joint x-ray and neutron diffraction'
'single-crystal joint x-ray and electron diffraction'
'solution nmr'
'solid-state nmr'
'theoretical model'
other
save_
save__exptl.method_details
_definition.id '_exptl.method_details'
loop_
_alias.definition_id
'_exptl.method_details'
_definition.update 2014-06-12
_description.text
;
A description of special aspects of the experimental method.
;
_name.category_id exptl
_name.object_id method_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'29 structures'
'minimized average structure'
save_
save__exptl.special_details
_definition.id '_exptl.special_details'
loop_
_alias.definition_id
'_exptl.special_details'
'_exptl_special_details'
'_exptl.details'
_definition.update 2012-11-22
_description.text
;
Details of the experiment prior to intensity measurement.
See also _exptl_crystal.preparation
;
_name.category_id exptl
_name.object_id special_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__exptl.transmission_factor_max
_definition.id '_exptl.transmission_factor_max'
loop_
_alias.definition_id
'_exptl.transmission_factor_max'
'_exptl_transmission_factor_max'
_definition.update 2013-04-11
_description.text
;
The calculated maximum value of the transmission factor for
the specimen. Its value does not include the effects of
absorption in the specimen mount. The presence of this
item does not imply that the structure factors have been
corrected for absorption. For the applied correction see
_exptl_absorpt.correction_T_max.
;
_name.category_id exptl
_name.object_id transmission_factor_max
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save__exptl.transmission_factor_min
_definition.id '_exptl.transmission_factor_min'
loop_
_alias.definition_id
'_exptl.transmission_factor_min'
'_exptl_transmission_factor_min'
_definition.update 2013-04-11
_description.text
;
The calculated minimum value of the transmission factor for
the specimen. Its value does not include the effects of
absorption in the specimen mount. The presence of this
item does not imply that the structure factors have been
corrected for absorption. For the applied correction see
_exptl_absorpt.correction_T_max.
;
_name.category_id exptl
_name.object_id transmission_factor_min
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save_CELL
_definition.id CELL
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items used to describe the parameters of
the crystal unit cell and their measurement.
;
_name.category_id EXPTL
_name.object_id CELL
save_
save__cell.atomic_mass
_definition.id '_cell.atomic_mass'
loop_
_alias.definition_id
'_cell.atomic_mass'
_definition.update 2012-11-22
_description.text
;
Atomic mass of the contents of the unit cell. This calculated
from the atom sites present in the ATOM_TYPE list, rather than
the ATOM_SITE lists of atoms in the refined model.
;
_name.category_id cell
_name.object_id atomic_mass
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code dalton
loop_
_method.purpose
_method.expression
Evaluation
;
mass = 0.
Loop t as atom_type {
mass += t.number_in_cell * t.atomic_mass
}
_cell.atomic_mass = mass
;
save_
save__cell.formula_units_Z
_definition.id '_cell.formula_units_Z'
loop_
_alias.definition_id
'_cell.formula_units_Z'
'_cell_formula_units_Z'
_definition.update 2012-11-22
_description.text
;
The number of the formula units in the unit cell as specified
by _chemical_formula.structural, _chemical_formula.moiety or
_chemical_formula.sum.
;
_name.category_id cell
_name.object_id formula_units_Z
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Count
_enumeration.range 1:
save_
save__cell.metric_tensor
_definition.id '_cell.metric_tensor'
loop_
_alias.definition_id
'_cell.metric_tensor'
_definition.update 2012-11-22
_description.text
;
The direct space (covariant) metric tensor used to transform
vectors and coordinates from real (direct) to reciprocal space.
;
_name.category_id cell
_name.object_id metric_tensor
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3 3]
loop_
_method.purpose
_method.expression
Evaluation
;
with v as cell_vector
_cell.metric_tensor = [[ v.a*v.a, v.a*v.b, v.a*v.c ],
[ v.b*v.a, v.b*v.b, v.b*v.c ],
[ v.c*v.a, v.c*v.b, v.c*v.c ]]
;
save_
save__cell.orthogonal_matrix
_definition.id '_cell.orthogonal_matrix'
loop_
_alias.definition_id
'_cell.orthogonal_matrix'
_definition.update 2012-11-22
_description.text
;
Orthogonal matrix of the crystal unit cell. Definition uses
Rollet's axial assignments with cell vectors a,b,c aligned
with orthogonal axes X,Y,Z so that c||Z and b in plane YZ.
;
_name.category_id cell
_name.object_id orthogonal_matrix
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3 3]
loop_
_method.purpose
_method.expression
Evaluation
;
With p as cell_length
With q as cell_angle
With r as cell_reciprocal_angle
_cell.orthogonal_matrix = [
[ p.a*Sind(q.beta)*Sind(r.gamma), 0, 0 ],
[ -p.a*Sind(q.beta)*Cosd(r.gamma), p.b*Sind(q.alpha), 0 ],
[ p.a*Cosd(q.beta), p.b*Cosd(q.alpha), p.c ]]
;
save_
save__cell.special_details
_definition.id '_cell.special_details'
loop_
_alias.definition_id
'_cell.special_details'
'_cell_special_details'
'_cell.details'
_definition.update 2012-11-22
_description.text
;
Description of special aspects of the cell choice, noting
possible alternative settings.
;
_name.category_id cell
_name.object_id special_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__cell.volume
_definition.id '_cell.volume'
loop_
_alias.definition_id
'_cell.volume'
'_cell_volume'
_definition.update 2013-03-07
_description.text
;
Volume of the crystal unit cell.
;
_name.category_id cell
_name.object_id volume
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstrom_cubed
loop_
_method.purpose
_method.expression
Evaluation
;
With v as cell_vector
_cell.volume = v.a * ( v.b ^ v.c )
;
save_
save__cell.volume_su
_definition.id '_cell.volume_su'
loop_
_alias.definition_id
'_cell.volume_su'
'_cell_volume_su'
'_cell.volume_esd'
_definition.update 2014-06-08
_description.text
;
Standard uncertainty of the volume of the crystal unit cell.
;
_name.category_id cell
_name.object_id volume_su
_name.linked_item_id '_cell.volume'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstrom_cubed
save_
save_CELL_ANGLE
_definition.id CELL_ANGLE
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items used to describe the angles between
the axes in the crystal unit cell.
;
_name.category_id CELL
_name.object_id CELL_ANGLE
save_
save__cell_angle.alpha
_definition.id '_cell_angle.alpha'
loop_
_alias.definition_id
'_cell_angle.alpha'
'_cell_angle_alpha'
'_cell.angle_alpha'
_name.category_id cell_angle
_name.object_id alpha
_type.contents Real
_type.purpose Measurand
_description.text
;
The angle between the bounding cell axes.
;
_enumeration.range 0.0:180.0
_type.source Recorded
_type.container Single
_definition.update 2014-06-08
_units.code degrees
_enumeration.default 90.0
save_
save__cell_angle.alpha_su
_definition.id '_cell_angle.alpha_su'
loop_
_alias.definition_id
'_cell_angle.alpha_su'
'_cell_angle_alpha_su'
'_cell.angle_alpha_esd'
_name.category_id cell_angle
_name.object_id alpha_su
_name.linked_item_id '_cell_angle.alpha'
_type.contents Real
_type.purpose SU
_description.text
;
Standard uncertainty of the angle between the bounding cell axes.
;
_enumeration.range 0.0:180.0
_type.source Recorded
_type.container Single
_definition.update 2014-06-08
_units.code degrees
_enumeration.default 90.0
save_
save__cell_angle.beta
_definition.id '_cell_angle.beta'
loop_
_alias.definition_id
'_cell_angle.beta'
'_cell_angle_beta'
'_cell.angle_beta'
_name.category_id cell_angle
_name.object_id beta
_type.contents Real
_type.purpose Measurand
_description.text
;
The angle between the bounding cell axes.
;
_enumeration.range 0.0:180.0
_type.source Recorded
_type.container Single
_definition.update 2014-06-08
_units.code degrees
_enumeration.default 90.0
save_
save__cell_angle.beta_su
_definition.id '_cell_angle.beta_su'
loop_
_alias.definition_id
'_cell_angle.beta_su'
'_cell_angle_beta_su'
'_cell.angle_beta_esd'
_name.category_id cell_angle
_name.object_id beta_su
_name.linked_item_id '_cell_angle.beta'
_type.contents Real
_type.purpose SU
_description.text
;
Standard uncertainty of the angle between the bounding cell axes.
;
_enumeration.range 0.0:180.0
_type.source Recorded
_type.container Single
_definition.update 2014-06-08
_units.code degrees
_enumeration.default 90.0
save_
save__cell_angle.gamma
_definition.id '_cell_angle.gamma'
loop_
_alias.definition_id
'_cell_angle.gamma'
'_cell_angle_gamma'
'_cell.angle_gamma'
_name.category_id cell_angle
_name.object_id gamma
_type.contents Real
_type.purpose Measurand
_description.text
;
The angle between the bounding cell axes.
;
_enumeration.range 0.0:180.0
_type.source Recorded
_type.container Single
_definition.update 2014-06-08
_units.code degrees
_enumeration.default 90.0
save_
save__cell_angle.gamma_su
_definition.id '_cell_angle.gamma_su'
loop_
_alias.definition_id
'_cell_angle.gamma_su'
'_cell_angle_gamma_su'
'_cell.angle_gamma_esd'
_name.category_id cell_angle
_name.object_id gamma_su
_name.linked_item_id '_cell_angle.gamma'
_type.contents Real
_type.purpose SU
_description.text
;
Standard uncertainty of the angle between the bounding cell axes.
;
_enumeration.range 0.0:180.0
_type.source Recorded
_type.container Single
_definition.update 2014-06-08
_units.code degrees
_enumeration.default 90.0
save_
save_CELL_LENGTH
_definition.id CELL_LENGTH
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items used to describe the lengths of
the axes in the crystal unit cell.
;
_name.category_id CELL
_name.object_id CELL_LENGTH
save_
save__cell_length.a
_definition.id '_cell_length.a'
loop_
_alias.definition_id
'_cell_length.a'
'_cell_length_a'
'_cell.length_a'
_name.category_id cell_length
_name.object_id a
_type.contents Real
_type.purpose Measurand
_description.text
;
The length of each cell axis.
;
_enumeration.range 1.:
_type.source Recorded
_type.container Single
_definition.update 2014-06-08
_units.code angstroms
save_
save__cell_length.a_su
_definition.id '_cell_length.a_su'
loop_
_alias.definition_id
'_cell_length.a_su'
'_cell_length_a_su'
'_cell.length_a_esd'
_name.category_id cell_length
_name.object_id a_su
_name.linked_item_id '_cell_length.a'
_type.contents Real
_type.purpose SU
_description.text
;
Standard uncertainty of the length of each cell axis.
;
_enumeration.range 0.:
_type.source Recorded
_type.container Single
_definition.update 2014-06-08
_units.code angstroms
_enumeration.default 0.0
save_
save__cell_length.b
_definition.id '_cell_length.b'
loop_
_alias.definition_id
'_cell_length.b'
'_cell_length_b'
'_cell.length_b'
_name.category_id cell_length
_name.object_id b
_type.contents Real
_type.purpose Measurand
_description.text
;
The length of each cell axis.
;
_enumeration.range 1.:
_type.source Recorded
_type.container Single
_definition.update 2014-06-08
_units.code angstroms
save_
save__cell_length.b_su
_definition.id '_cell_length.b_su'
loop_
_alias.definition_id
'_cell_length.b_su'
'_cell_length_b_su'
'_cell.length_b_esd'
_name.category_id cell_length
_name.object_id b_su
_name.linked_item_id '_cell_length.b'
_type.contents Real
_type.purpose SU
_description.text
;
Standard uncertainty of the length of each cell axis.
;
_enumeration.range 0.:
_type.source Recorded
_type.container Single
_definition.update 2014-06-08
_units.code angstroms
_enumeration.default 0.0
save_
save__cell_length.c
_definition.id '_cell_length.c'
loop_
_alias.definition_id
'_cell_length.c'
'_cell_length_c'
'_cell.length_c'
_name.category_id cell_length
_name.object_id c
_type.contents Real
_type.purpose Measurand
_description.text
;
The length of each cell axis.
;
_enumeration.range 1.:
_type.source Recorded
_type.container Single
_definition.update 2014-06-08
_units.code angstroms
save_
save__cell_length.c_su
_definition.id '_cell_length.c_su'
loop_
_alias.definition_id
'_cell_length.c_su'
'_cell_length_c_su'
'_cell.length_c_esd'
_name.category_id cell_length
_name.object_id c_su
_name.linked_item_id '_cell_length.c'
_type.contents Real
_type.purpose SU
_description.text
;
Standard uncertainty of the length of each cell axis.
;
_enumeration.range 0.:
_type.source Recorded
_type.container Single
_definition.update 2014-06-08
_units.code angstroms
_enumeration.default 0.0
save_
save_CELL_MEASUREMENT
_definition.id CELL_MEASUREMENT
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items used to describe the angles between
the axes in the crystal unit cell.
;
_name.category_id CELL
_name.object_id CELL_MEASUREMENT
save_
save__cell_measurement.pressure
_definition.id '_cell_measurement.pressure'
loop_
_alias.definition_id
'_cell_measurement.pressure'
'_cell_measurement_pressure'
_definition.update 2012-11-22
_description.text
;
The pressure at which the unit-cell parameters were measured
(not the pressure used to synthesize the sample).
;
_name.category_id cell_measurement
_name.object_id pressure
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kilopascals
save_
save__cell_measurement.pressure_su
_definition.id '_cell_measurement.pressure_su'
loop_
_alias.definition_id
'_cell_measurement.pressure_su'
'_cell_measurement_pressure_su'
'_cell_measurement.pressure_esd'
_definition.update 2014-06-08
_description.text
;
The standard uncertainty value that the temperature of
the pressure at which the unit-cell parameters were measured
;
_name.category_id cell_measurement
_name.object_id pressure_su
_name.linked_item_id '_cell_measurement.pressure'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kilopascals
save_
save__cell_measurement.radiation
_definition.id '_cell_measurement.radiation'
loop_
_alias.definition_id
'_cell_measurement.radiation'
'_cell_measurement_radiation'
_definition.update 2012-11-22
_description.text
;
Description of the radiation used to measure the unit-cell data.
;
_name.category_id cell_measurement
_name.object_id radiation
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
neutron
'X-ray tube'
synchrotron
save_
save__cell_measurement.reflns_used
_definition.id '_cell_measurement.reflns_used'
loop_
_alias.definition_id
'_cell_measurement.reflns_used'
'_cell_measurement_reflns_used'
_definition.update 2012-11-22
_description.text
;
Total number of reflections used to determine the unit cell.
The reflections may be specified as cell_measurement_refln items.
;
_name.category_id cell_measurement
_name.object_id reflns_used
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Count
_enumeration.range 3:
save_
save__cell_measurement.temperature
_definition.id '_cell_measurement.temperature'
loop_
_alias.definition_id
'_cell_measurement.temperature'
'_cell_measurement_temperature'
'_cell_measurement_temp'
'_cell_measurement.temp'
_definition.update 2012-11-22
_description.text
;
The temperature at which the unit-cell parameters were measured
(not the temperature of synthesis).
;
_name.category_id cell_measurement
_name.object_id temperature
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__cell_measurement.temperature_su
_definition.id '_cell_measurement.temperature_su'
loop_
_alias.definition_id
'_cell_measurement.temperature_su'
'_cell_measurement_temp_su'
'_cell_measurement.temp_esd'
_definition.update 2012-11-22
_description.text
;
The standard uncertainty value that the temperature of
the unit-cell parameters were measured
;
_name.category_id cell_measurement
_name.object_id temperature_su
_name.linked_item_id '_cell_measurement.temperature'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__cell_measurement.theta_max
_definition.id '_cell_measurement.theta_max'
loop_
_alias.definition_id
'_cell_measurement.theta_max'
'_cell_measurement_theta_max'
_definition.update 2012-11-22
_description.text
;
Maximum theta scattering angle of reflections used to measure
the crystal unit cell.
;
_name.category_id cell_measurement
_name.object_id theta_max
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:90.0
_units.code degrees
save_
save__cell_measurement.theta_min
_definition.id '_cell_measurement.theta_min'
loop_
_alias.definition_id
'_cell_measurement.theta_min'
'_cell_measurement_theta_min'
_definition.update 2012-11-22
_description.text
;
Minimum theta scattering angle of reflections used to measure
the crystal unit cell.
;
_name.category_id cell_measurement
_name.object_id theta_min
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:90.0
_units.code degrees
save_
save__cell_measurement.wavelength
_definition.id '_cell_measurement.wavelength'
loop_
_alias.definition_id
'_cell_measurement.wavelength'
'_cell_measurement_wavelength'
_definition.update 2012-11-22
_description.text
;
Wavelength of the radiation used to measure the unit cell.
If this is not specified, the wavelength is assumed to be the
same as that given in _diffrn_radiation_wavelength.value
;
_name.category_id cell_measurement
_name.object_id wavelength
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save_CELL_MEASUREMENT_REFLN
_definition.id CELL_MEASUREMENT_REFLN
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to describe the reflection data
used in the measurement of the crystal unit cell.
;
_name.category_id CELL_MEASUREMENT
_name.object_id CELL_MEASUREMENT_REFLN
_category.key_id '_cell_measurement_refln.key'
_category.key_list ['_cell_measurement_refln.index_h'
'_cell_measurement_refln.index_k'
'_cell_measurement_refln.index_l']
save_
save__cell_measurement_refln.hkl
_definition.id '_cell_measurement_refln.hkl'
loop_
_alias.definition_id
'_cell_measurement_refln.hkl'
_definition.update 2012-11-22
_description.text
;
Miller indices of a reflection used to measure the unit cell.
;
_name.category_id cell_measurement_refln
_name.object_id hkl
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Integer
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With c as cell_measurement_refln
_cell_measurement_refln.hkl = [c.index_h, c.index_k, c.index_l]
;
save_
save__cell_measurement_refln.index_h
_definition.id '_cell_measurement_refln.index_h'
loop_
_alias.definition_id
'_cell_measurement_refln.index_h'
'_cell_measurement_refln_index_h'
_name.category_id cell_measurement_refln
_name.object_id index_h
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__cell_measurement_refln.index_k
_definition.id '_cell_measurement_refln.index_k'
loop_
_alias.definition_id
'_cell_measurement_refln.index_k'
'_cell_measurement_refln_index_k'
_name.category_id cell_measurement_refln
_name.object_id index_k
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__cell_measurement_refln.index_l
_definition.id '_cell_measurement_refln.index_l'
loop_
_alias.definition_id
'_cell_measurement_refln.index_l'
'_cell_measurement_refln_index_l'
_name.category_id cell_measurement_refln
_name.object_id index_l
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__cell_measurement_refln.key
_definition.id '_cell_measurement_refln.key'
loop_
_alias.definition_id
'_cell_measurement_refln.key'
_definition.update 2012-11-22
_description.text
;
Value is a unique key to a set of CELL_MEASUREMENT_REFLN items
in a looped list.
;
_name.category_id cell_measurement_refln
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Integer
loop_
_method.purpose
_method.expression
Evaluation ' _cell_measurement_refln.key = _cell_measurement_refln.hkl'
save_
save__cell_measurement_refln.theta
_definition.id '_cell_measurement_refln.theta'
loop_
_alias.definition_id
'_cell_measurement_refln.theta'
'_cell_measurement_refln_theta'
_definition.update 2012-11-22
_description.text
;
Theta angle of reflection used to measure the crystal unit cell.
;
_name.category_id cell_measurement_refln
_name.object_id theta
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:90.0
_units.code degrees
save_
save_CELL_RECIPROCAL
_definition.id CELL_RECIPROCAL
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items used to describe the unit cell data
in reciprocal space.
;
_name.category_id CELL
_name.object_id CELL_RECIPROCAL
save_
save__cell_reciprocal.convert_Uij_to_betaij
_definition.id '_cell_reciprocal.convert_Uij_to_betaij'
loop_
_alias.definition_id
'_cell_reciprocal.convert_Uij_to_betaij'
_definition.update 2013-04-28
_description.text
;
The reciprocal space matrix for converting the U(ij) matrix of
atomic displacement parameters to a dimensionless beta(IJ) matrix.
The adp factor in a structure factor expression:
t = exp -2pi**2 ( U11 h h a* a* + ...... 2 U23 k l b* c* )
t = exp - 0.25 ( B11 h h a* a* + ...... 2 B23 k l b* c* )
= exp - ( beta11 h h + ............ 2 beta23 k l )
The conversion of the U or B matrices to the beta matrix
beta = C U C = C B C /8pi**2
where C is conversion matrix defined here.
;
_name.category_id cell_reciprocal
_name.object_id convert_Uij_to_betaij
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3 3]
loop_
_method.purpose
_method.expression
Evaluation
;
With r as cell_reciprocal_length
_cell_reciprocal.convert_Uij_to_betaij = \
1.4142 * Pi * Matrix([[ r.a, 0, 0 ],
[ 0, r.b, 0 ],
[ 0, 0, r.c ]])
;
save_
save__cell_reciprocal.convert_Uiso_to_Uij
_definition.id '_cell_reciprocal.convert_Uiso_to_Uij'
loop_
_alias.definition_id
'_cell_reciprocal.convert_Uiso_to_Uij'
_definition.update 2013-04-28
_description.text
;
The reciprocal space matrix for converting the isotropic Uiso
atomic displacement parameter to the anisotropic matrix Uij.
| 1 cos(gamma*) cos(beta*) |
U[i,j] = Uiso * | cos(gamma*) 1 cos(alpha*) |
| cos(beta*) cos(alpha*) 1 |
;
_name.category_id cell_reciprocal
_name.object_id convert_Uiso_to_Uij
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3 3]
loop_
_method.purpose
_method.expression
Evaluation
;
With r as cell_reciprocal_angle
_cell_reciprocal.convert_Uiso_to_Uij = \
[[ 1., Cosd(r.gamma), Cosd(r.beta) ],
[ Cosd(r.gamma), 1., Cosd(r.alpha) ],
[ Cosd(r.beta), Cosd(r.alpha), 1. ]]
;
save_
save__cell_reciprocal.metric_tensor
_definition.id '_cell_reciprocal.metric_tensor'
loop_
_alias.definition_id
'_cell_reciprocal.metric_tensor'
_definition.update 2012-11-22
_description.text
;
The reciprocal (contravariant) metric tensor used to transform
vectors and coordinates from reciprocal space to real (direct)
space.
;
_name.category_id cell_reciprocal
_name.object_id metric_tensor
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3 3]
loop_
_method.purpose
_method.expression
Evaluation
;
with r as cell_reciprocal_vector
_cell_reciprocal.metric_tensor = [[ r.a*r.a, r.a*r.b, r.a*r.c ],
[ r.b*r.a, r.b*r.b, r.b*r.c ],
[ r.c*r.a, r.c*r.b, r.c*r.c ]]
;
save_
save__cell_reciprocal.orthogonal_matrix
_definition.id '_cell_reciprocal.orthogonal_matrix'
loop_
_alias.definition_id
'_cell_reciprocal.orthogonal_matrix'
_definition.update 2012-11-22
_description.text
;
Orthogonal matrix of the reciprocal space. The matrix may be
used to transform the non-orthogonal vector h = (h,k,l) into
the orthogonal indices p = (p,q,r)
M h = p
;
_name.category_id cell_reciprocal
_name.object_id orthogonal_matrix
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3 3]
loop_
_method.purpose
_method.expression
Evaluation
;
_cell_reciprocal.orthogonal_matrix = Inverse(
Transpose( _cell.orthogonal_matrix ))
;
save_
save_CELL_RECIPROCAL_ANGLE
_definition.id CELL_RECIPROCAL_ANGLE
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items used to describe the unit cell angles
in reciprocal space.
;
_name.category_id CELL_RECIPROCAL
_name.object_id CELL_RECIPROCAL_ANGLE
save_
save__cell_reciprocal_angle.alpha
_definition.id '_cell_reciprocal_angle.alpha'
loop_
_alias.definition_id
'_cell_reciprocal_angle.alpha'
'_cell_reciprocal_angle_alpha'
'_cell.reciprocal_angle_alpha'
_definition.update 2013-01-18
_description.text
;
Reciprocal of the angle between _cell_length.b and _cell_length.c.
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
;
_name.category_id cell_reciprocal_angle
_name.object_id alpha
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:180.
_units.code degrees
loop_
_method.purpose
_method.expression
Evaluation
;
With c as cell_angle
_cell_reciprocal_angle.alpha = Acosd(
(Cosd(c.beta)*Cosd(c.gamma)-Cosd(c.alpha))/(Sind(c.beta)*Sind(c.gamma)))
;
save_
save__cell_reciprocal_angle.alpha_su
_definition.id '_cell_reciprocal_angle.alpha_su'
loop_
_alias.definition_id
'_cell_reciprocal_angle.alpha_su'
'_cell_reciprocal_angle_alpha_su'
'_cell.reciprocal_angle_alpha_esd'
_definition.update 2013-01-18
_description.text
;
Standard Uncertainty of the
Reciprocal of the angle between _cell_length.b and _cell_length.c.
;
_name.category_id cell_reciprocal_angle
_name.object_id alpha_su
_name.linked_item_id '_cell_reciprocal_angle.alpha'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.:180.
_units.code degrees
save_
save__cell_reciprocal_angle.beta
_definition.id '_cell_reciprocal_angle.beta'
loop_
_alias.definition_id
'_cell_reciprocal_angle.beta'
'_cell_reciprocal_angle_beta'
'_cell.reciprocal_angle_beta'
_definition.update 2013-01-18
_description.text
;
Reciprocal of the angle between _cell_length.a and _cell_length.c.
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
;
_name.category_id cell_reciprocal_angle
_name.object_id beta
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:180.
_units.code degrees
loop_
_method.purpose
_method.expression
Evaluation
;
With c as cell_angle
_cell_reciprocal_angle.beta = Acosd(
(Cosd(c.alpha)*Cosd(c.gamma)-Cosd(c.beta))/(Sind(c.alpha)*Sind(c.gamma)))
;
save_
save__cell_reciprocal_angle.beta_su
_definition.id '_cell_reciprocal_angle.beta_su'
loop_
_alias.definition_id
'_cell_reciprocal_angle.beta_su'
'_cell_reciprocal_angle_beta_su'
'_cell.reciprocal_angle_beta_esd'
_definition.update 2013-01-18
_description.text
;
Standard Uncertainty of the
Reciprocal of the angle between _cell_length.a and _cell_length.c.
;
_name.category_id cell_reciprocal_angle
_name.object_id beta_su
_name.linked_item_id '_cell_reciprocal_angle.beta'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.:180.
_units.code degrees
save_
save__cell_reciprocal_angle.gamma
_definition.id '_cell_reciprocal_angle.gamma'
loop_
_alias.definition_id
'_cell_reciprocal_angle.gamma'
'_cell_reciprocal_angle_gamma'
'_cell.reciprocal_angle_gamma'
_definition.update 2013-01-18
_description.text
;
Reciprocal of the angle between _cell_length.a and _cell_length.b.
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
;
_name.category_id cell_reciprocal_angle
_name.object_id gamma
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:180.
_units.code degrees
loop_
_method.purpose
_method.expression
Evaluation
;
With c as cell_angle
_cell_reciprocal_angle.gamma = Acosd(
(Cosd(c.alpha)*Cosd(c.beta)-Cosd(c.gamma))/(Sind(c.alpha)*Sind(c.beta)))
;
save_
save__cell_reciprocal_angle.gamma_su
_definition.id '_cell_reciprocal_angle.gamma_su'
loop_
_alias.definition_id
'_cell_reciprocal_angle.gamma_su'
'_cell_reciprocal_angle_gamma_su'
'_cell.reciprocal_angle_gamma_esd'
_definition.update 2013-01-18
_description.text
;
Standard Uncertainty of the
Reciprocal of the angle between _cell_length.a and _cell_length.b.
;
_name.category_id cell_reciprocal_angle
_name.object_id gamma_su
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:180.
_units.code degrees
save_
save_CELL_RECIPROCAL_LENGTH
_definition.id CELL_RECIPROCAL_LENGTH
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items used to describe the unit cell lengths
in reciprocal space.
;
_name.category_id CELL_RECIPROCAL
_name.object_id CELL_RECIPROCAL_LENGTH
save_
save__cell_reciprocal_length.a
_definition.id '_cell_reciprocal_length.a'
loop_
_alias.definition_id
'_cell_reciprocal_length.a'
'_cell_reciprocal_length_a'
'_cell.reciprocal_length_a'
_definition.update 2012-11-22
_description.text
;
Reciprocal of the _cell_length.a.
;
_name.category_id cell_reciprocal_length
_name.object_id a
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code reciprocal_angstroms
loop_
_method.purpose
_method.expression
Evaluation
;
_cell_reciprocal_length.a = Norm ( _cell_reciprocal_vector.a )
;
save_
save__cell_reciprocal_length.a_su
_definition.id '_cell_reciprocal_length.a_su'
loop_
_alias.definition_id
'_cell_reciprocal_length.a_su'
'_cell_reciprocal_length_a_su'
'_cell.reciprocal_length_a_esd'
_definition.update 2012-11-22
_description.text
;
Standard Uncertainty of the reciprocal of the _cell_length.a.
;
_name.category_id cell_reciprocal_length
_name.object_id a_su
_name.linked_item_id '_cell_reciprocal_length.a'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code reciprocal_angstroms
save_
save__cell_reciprocal_length.b
_definition.id '_cell_reciprocal_length.b'
loop_
_alias.definition_id
'_cell_reciprocal_length.b'
'_cell_reciprocal_length_b'
'_cell.reciprocal_length_b'
_definition.update 2012-11-22
_description.text
;
Reciprocal of the _cell_length.b.
;
_name.category_id cell_reciprocal_length
_name.object_id b
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code reciprocal_angstroms
loop_
_method.purpose
_method.expression
Evaluation
;
_cell_reciprocal_length.b = Norm ( _cell_reciprocal_vector.b )
;
save_
save__cell_reciprocal_length.b_su
_definition.id '_cell_reciprocal_length.b_su'
loop_
_alias.definition_id
'_cell_reciprocal_length.b_su'
'_cell_reciprocal_length_b_su'
'_cell.reciprocal_length_b_esd'
_definition.update 2012-11-22
_description.text
;
Standard Uncertainty of the reciprocal of the _cell_length.b.
;
_name.category_id cell_reciprocal_length
_name.object_id b_su
_name.linked_item_id '_cell_reciprocal_length.b'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code reciprocal_angstroms
save_
save__cell_reciprocal_length.c
_definition.id '_cell_reciprocal_length.c'
loop_
_alias.definition_id
'_cell_reciprocal_length.c'
'_cell_reciprocal_length_c'
'_cell.reciprocal_length_c'
_definition.update 2012-11-22
_description.text
;
Reciprocal of the _cell_length.c.
;
_name.category_id cell_reciprocal_length
_name.object_id c
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code reciprocal_angstroms
loop_
_method.purpose
_method.expression
Evaluation
;
_cell_reciprocal_length.c = Norm ( _cell_reciprocal_vector.c )
;
save_
save__cell_reciprocal_length.c_su
_definition.id '_cell_reciprocal_length.c_su'
loop_
_alias.definition_id
'_cell_reciprocal_length.c_su'
'_cell_reciprocal_length_c_su'
'_cell.reciprocal_length_c_esd'
_definition.update 2012-11-22
_description.text
;
Standard Uncertainty of the reciprocal of the _cell_length.c.
;
_name.category_id cell_reciprocal_length
_name.object_id c_su
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code reciprocal_angstroms
save_
save_CELL_RECIPROCAL_VECTOR
_definition.id CELL_RECIPROCAL_VECTOR
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items used to describe the unit cell vectors
in reciprocal space.
;
_name.category_id CELL_RECIPROCAL
_name.object_id CELL_RECIPROCAL_VECTOR
save_
save__cell_reciprocal_vector.a
_definition.id '_cell_reciprocal_vector.a'
loop_
_alias.definition_id
'_cell_reciprocal_vector.a'
_definition.update 2012-11-22
_description.text
;
Reciprocal of the _cell_vector.a.
;
_name.category_id cell_reciprocal_vector
_name.object_id a
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With c as cell_vector
_cell_reciprocal_vector.a = c.b ^ c.c / _cell.volume
;
save_
save__cell_reciprocal_vector.b
_definition.id '_cell_reciprocal_vector.b'
loop_
_alias.definition_id
'_cell_reciprocal_vector.b'
_definition.update 2012-11-22
_description.text
;
Reciprocal of the _cell_vector.b.
;
_name.category_id cell_reciprocal_vector
_name.object_id b
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With c as cell_vector
_cell_reciprocal_vector.b = c.c ^ c.a / _cell.volume
;
save_
save__cell_reciprocal_vector.c
_definition.id '_cell_reciprocal_vector.c'
loop_
_alias.definition_id
'_cell_reciprocal_vector.c'
_definition.update 2012-11-22
_description.text
;
Reciprocal of the _cell_vector.c.
;
_name.category_id cell_reciprocal_vector
_name.object_id c
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With c as cell_vector
_cell_reciprocal_vector.c = c.a ^ c.b / _cell.volume
;
save_
save_CELL_VECTOR
_definition.id CELL_VECTOR
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items used to describe the axial vectors of
the crystal unit cell.
;
_name.category_id CELL
_name.object_id CELL_VECTOR
save_
save__cell_vector.a
_definition.id '_cell_vector.a'
loop_
_alias.definition_id
'_cell_vector.a'
_definition.update 2012-11-22
_description.text
;
The cell vector along the x axis.
;
_name.category_id cell_vector
_name.object_id a
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
_cell_vector.a = _cell.orthogonal_matrix * Matrix([1,0,0])
;
save_
save__cell_vector.b
_definition.id '_cell_vector.b'
loop_
_alias.definition_id
'_cell_vector.b'
_definition.update 2012-11-22
_description.text
;
The cell vector along the y axis.
;
_name.category_id cell_vector
_name.object_id b
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
_cell_vector.b = _cell.orthogonal_matrix * Matrix([0,1,0])
;
save_
save__cell_vector.c
_definition.id '_cell_vector.c'
loop_
_alias.definition_id
'_cell_vector.c'
_definition.update 2012-11-22
_description.text
;
The cell vector along the z axis.
;
_name.category_id cell_vector
_name.object_id c
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
_cell_vector.c = _cell.orthogonal_matrix * Matrix([0,0,1])
;
save_
save_CHEMICAL
_definition.id CHEMICAL
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items which describe the composition and
chemical properties of the compound under study. The formula data
items must be consistent with the density, unit-cell and Z values.
;
_name.category_id EXPTL
_name.object_id CHEMICAL
save_
save__chemical.absolute_configuration
_definition.id '_chemical.absolute_configuration'
loop_
_alias.definition_id
'_chemical.absolute_configuration'
'_chemical_absolute_configuration'
_definition.update 2012-11-22
_description.text
;
Necessary conditions for this assignment are given by
Flack, H. D. & Bernardinelli, G. (1999). Acta Cryst. A55,
908-915. (http://www.iucr.org/paper?sh0129)
Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst.
33, 1143-1148. (http://www.iucr.org/paper?ks0021)
;
_name.category_id chemical
_name.object_id absolute_configuration
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
rm
; 'reference molecule' Absolute configuration established by
the structure determination of a compound containing a
chiral reference molecule of known absolute configuration.
;
ad
; 'anomalous dispersion' Absolute configuration established by
a-d effects in diffraction measurements on the crystal.
;
rmad
; 'rm + ad' Absolute configuration established by the structure
determination of a compound containing a chiral reference
molecule of known absolute configuration and confirmed by
a-d effects in diffraction measurements on the crystal.
;
syn
; 'synthetic' Absolute configuration has not been established
by anomalous-dispersion effects in diffraction measurements on
the crystal. The enantiomer has been assigned by reference to
an unchanging chiral centre in the synthetic procedure.
;
unk
; 'unknown' No firm chemical or a-d evidence for an assignment
is available. An arbitrary choice of enantiomer has been made.
;
. inapplicable
_enumeration.default .
save_
save__chemical.compound_source
_definition.id '_chemical.compound_source'
loop_
_alias.definition_id
'_chemical.compound_source'
'_chemical_compound_source'
_definition.update 2012-11-22
_description.text
;
Description of the source of the compound under study, or of the
parent molecule if a simple derivative is studied. This includes
the place of discovery for minerals or the actual source of a
natural product.
;
_name.category_id chemical
_name.object_id compound_source
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__chemical.enantioexcess_bulk
_definition.id '_chemical.enantioexcess_bulk'
loop_
_alias.definition_id
'_chemical.enantioexcess_bulk'
'_chemical_enantioexcess_bulk'
_definition.update 2013-01-18
_description.text
;
The enantioexcess of the bulk material from which the crystals
were grown. A value of 0.0 indicates the racemate. A value of
1.0 indicates that the compound is enantiomerically pure.
Enantioexcess is defined in the IUPAC Recommendations
(Moss et al., 1996). The composition of the crystal
and bulk must be the same.
Ref: Moss G. P. et al. (1996). Basic Terminology of
Stereochemistry. Pure Appl. Chem., 68, 2193-2222.
http://www.chem.qmul.ac.uk/iupac/stereo/index.html
;
_name.category_id chemical
_name.object_id enantioexcess_bulk
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save__chemical.enantioexcess_bulk_technique
_definition.id '_chemical.enantioexcess_bulk_technique'
loop_
_alias.definition_id
'_chemical.enantioexcess_bulk_technique'
'_chemical_enantioexcess_bulk_technique'
_definition.update 2013-01-18
_description.text
;
Technique used to determine the enantioexcess of the bulk compound.
;
_name.category_id chemical
_name.object_id enantioexcess_bulk_technique
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
OA
; Enantioexcess determined by measurement of the specific rotation
of the optical activity of the bulk compound in solution.
;
CD
; Enantioexcess determined by measurement of the visible/near UV
circular dichroism spectrum of the bulk compound in solution.
;
EC
; Enantioexcess determined by enantioselective chromatography of
the bulk compound in solution.
;
other ' Enantioexcess determined by a technique not in this list.'
_enumeration.default OA
save_
save__chemical.enantioexcess_crystal
_definition.id '_chemical.enantioexcess_crystal'
loop_
_alias.definition_id
'_chemical.enantioexcess_crystal'
'_chemical_enantioexcess_crystal'
_definition.update 2013-01-18
_description.text
;
The enantioexcess of the crystal used for the diffraction
study. A value of 0.0 indicates the racemate. A value of
1.0 indicates that the crystal is enantiomerically pure.
Enantioexcess is defined in the IUPAC Recommendations
(Moss et al., 1996).
Ref: Moss G. P. et al. (1996). Basic Terminology of
Stereochemistry. Pure Appl. Chem., 68, 2193-2222.
http://www.chem.qmul.ac.uk/iupac/stereo/index.html
;
_name.category_id chemical
_name.object_id enantioexcess_crystal
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save__chemical.enantioexcess_crystal_technique
_definition.id '_chemical.enantioexcess_crystal_technique'
loop_
_alias.definition_id
'_chemical.enantioexcess_crystal_technique'
'_chemical_enantioexcess_crystal_technique'
_definition.update 2013-01-18
_description.text
;
Technique used to determine the enantioexcess of the crystal.
;
_name.category_id chemical
_name.object_id enantioexcess_crystal_technique
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
CD
; Enantioexcess determined by measurement of the visible/near UV
circular dichroism spectrum of the crystal taken into solution.
;
EC
; Enantioexcess determined by enantioselective chromatography of
the crystal taken into solution.
;
other ' Enantioexcess determined by a technique not in this list.'
_enumeration.default CD
save_
save__chemical.identifier_inchi
_definition.id '_chemical.identifier_inchi'
loop_
_alias.definition_id
'_chemical.identifier_inchi'
'_chemical_identifier_inchi'
_definition.update 2013-01-18
_description.text
;
The IUPAC International Chemical Identifier (InChI) is a
textual identifier for chemical substances, designed to provide
a standard and human-readable way to encode molecular information
and to facilitate the search for such information in databases
and on the web.
Ref: McNaught, A. (2006). Chem. Int. (IUPAC), 28 (6), 12-14.
http://www.iupac.org/inchi/
;
_name.category_id chemical
_name.object_id identifier_inchi
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Text
loop_
_description_example.case
_description_example.detail
"InChI=1/C10H8/c1-2-6-10-8-4-3-7-9(10)5-1/h1-8H'" naphthalene
save_
save__chemical.identifier_inchi_key
_definition.id '_chemical.identifier_inchi_key'
loop_
_alias.definition_id
'_chemical.identifier_inchi_key'
'_chemical_identifier_inchi_key'
_definition.update 2013-01-18
_description.text
;
The InChIKey is a compact hashed version of the full InChI
(IUPAC International Chemical Identifier), designed to allow
for easy web searches of chemical compounds. See
http://www.iupac.org/inchi/
;
_name.category_id chemical
_name.object_id identifier_inchi_key
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Text
loop_
_description_example.case
_description_example.detail
InChIKey=OROGSEYTTFOCAN-DNJOTXNNBG codeine
save_
save__chemical.identifier_inchi_version
_definition.id '_chemical.identifier_inchi_version'
loop_
_alias.definition_id
'_chemical.identifier_inchi_version'
'_chemical_identifier_inchi_version'
_definition.update 2013-01-18
_description.text
;
Version number of the InChI standard to which the associated
chemical identifier string applies.
;
_name.category_id chemical
_name.object_id identifier_inchi_version
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_description_example.case
1.03
save_
save__chemical.melting_point
_definition.id '_chemical.melting_point'
loop_
_alias.definition_id
'_chemical.melting_point'
'_chemical_melting_point'
_definition.update 2012-11-22
_description.text
;
The temperature at which a crystalline solid changes to a liquid.
;
_name.category_id chemical
_name.object_id melting_point
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__chemical.melting_point_gt
_definition.id '_chemical.melting_point_gt'
loop_
_alias.definition_id
'_chemical.melting_point_gt'
'_chemical_melting_point_gt'
_definition.update 2012-12-11
_description.text
;
A temperature above which the melting point lies.
_chemical.melting_point should be used in preference where possible.
;
_name.category_id chemical
_name.object_id melting_point_gt
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__chemical.melting_point_lt
_definition.id '_chemical.melting_point_lt'
loop_
_alias.definition_id
'_chemical.melting_point_lt'
'_chemical_melting_point_lt'
_definition.update 2012-12-11
_description.text
;
A temperature below which the melting point lies.
_chemical.melting_point should be used in preference where possible.
;
_name.category_id chemical
_name.object_id melting_point_lt
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__chemical.name_common
_definition.id '_chemical.name_common'
loop_
_alias.definition_id
'_chemical.name_common'
'_chemical_name_common'
_definition.update 2012-11-22
_description.text
;
Trivial name by which the compound is commonly known.
;
_name.category_id chemical
_name.object_id name_common
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Text
save_
save__chemical.name_mineral
_definition.id '_chemical.name_mineral'
loop_
_alias.definition_id
'_chemical.name_mineral'
'_chemical_name_mineral'
_definition.update 2012-11-22
_description.text
;
Mineral name accepted by the International Mineralogical Association.
Use only for natural minerals.
;
_name.category_id chemical
_name.object_id name_mineral
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Text
save_
save__chemical.name_structure_type
_definition.id '_chemical.name_structure_type'
loop_
_alias.definition_id
'_chemical.name_structure_type'
'_chemical_name_structure_type'
_definition.update 2012-11-22
_description.text
;
Commonly used structure-type name. Usually only applied to
minerals or inorganic compounds.
;
_name.category_id chemical
_name.object_id name_structure_type
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Text
save_
save__chemical.name_systematic
_definition.id '_chemical.name_systematic'
loop_
_alias.definition_id
'_chemical.name_systematic'
'_chemical_name_systematic'
_definition.update 2012-11-22
_description.text
;
IUPAC or Chemical Abstracts full name of compound.
;
_name.category_id chemical
_name.object_id name_systematic
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Text
save_
save__chemical.optical_rotation
_definition.id '_chemical.optical_rotation'
loop_
_alias.definition_id
'_chemical.optical_rotation'
'_chemical_optical_rotation'
_definition.update 2012-11-22
_description.text
;
The optical rotation in solution of the compound is
specified in the following format:
'[\a]^TEMP^~WAVE~ = SORT (c = CONC, SOLV)'
where: TEMP is the temperature of the measurement in degrees Celsius,
WAVE is an indication of the wavelength of the light
used for the measurement,
CONC is the concentration of the solution given as the
mass of the substance in g in 100 ml of solution,
SORT is the signed value (preceded by a + or a - sign)
of 100.\a/(l.c), where \a is the signed optical
rotation in degrees measured in a cell of length l in
dm and c is the value of CONC in g, and
SOLV is the chemical formula of the solvent.
;
_name.category_id chemical
_name.object_id optical_rotation
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'[\a]^25^~D~ = +108 (c = 3.42, CHCl~3~)'
save_
save__chemical.properties_biological
_definition.id '_chemical.properties_biological'
loop_
_alias.definition_id
'_chemical.properties_biological'
'_chemical_properties_biological'
_definition.update 2012-12-11
_description.text
;
A description of the biological properties of the material.
;
_name.category_id chemical
_name.object_id properties_biological
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
; diverse biological activities including use as a laxative
and strong antibacterial activity against S. aureus and weak
activity against cyclooxygenase-1 (COX-1)
;
; antibiotic activity against Bacillus subtilis (ATCC 6051) but no
significant activity against Candida albicans (ATCC 14053),
Aspergillus flavus (NRRL 6541) & Fusarium verticillioides (NRRL 25457)
;
' weakly potent lipoxygenase nonredox inhibitor'
' no influenza A virus sialidase inhibitory & plaque reduction activities'
' low toxicity against Drosophila melanogaster'
save_
save__chemical.properties_physical
_definition.id '_chemical.properties_physical'
loop_
_alias.definition_id
'_chemical.properties_physical'
'_chemical_properties_physical'
_definition.update 2012-12-11
_description.text
;
A description of the physical properties of the material.
;
_name.category_id chemical
_name.object_id properties_physical
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
air-sensitive
moisture-sensitive
hygroscopic
deliquescent
oxygen-sensitive
photo-sensitive
pyrophoric
semiconductor
'ferromagnetic at low temperature'
'paramagnetic and thermochromic'
save_
save__chemical.temperature_decomposition
_definition.id '_chemical.temperature_decomposition'
loop_
_alias.definition_id
'_chemical.temperature_decomposition'
'_chemical_temperature_decomposition'
_definition.update 2012-12-11
_description.text
;
The temperature at which a crystalline solid decomposes.
;
_name.category_id chemical
_name.object_id temperature_decomposition
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__chemical.temperature_decomposition_gt
_definition.id '_chemical.temperature_decomposition_gt'
loop_
_alias.definition_id
'_chemical.temperature_decomposition_gt'
'_chemical_temperature_decomposition_gt'
_definition.update 2014-07-22
_description.text
;
The temperature above which a crystalline solid decomposes.
_chemical.temperature_decomposition should be used in preference.
;
_name.category_id chemical
_name.object_id temperature_decomposition_gt
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__chemical.temperature_decomposition_lt
_definition.id '_chemical.temperature_decomposition_lt'
loop_
_alias.definition_id
'_chemical.temperature_decomposition_lt'
'_chemical_temperature_decomposition_lt'
_definition.update 2012-12-11
_description.text
;
The temperature below which a crystalline solid decomposes.
_chemical.temperature_decomposition should be used in preference.
;
_name.category_id chemical
_name.object_id temperature_decomposition_lt
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__chemical.temperature_decomposition_su
_definition.id '_chemical.temperature_decomposition_su'
loop_
_alias.definition_id
'_chemical.temperature_decomposition_su'
'_chemical_temperature_decomposition_su'
'_chemical.temperature_decomposition_esd'
_definition.update 2012-12-11
_description.text
;
Standard Uncertainty of the
temperature at which a crystalline solid decomposes.
;
_name.category_id chemical
_name.object_id temperature_decomposition_su
_name.linked_item_id '_chemical.temperature_decomposition'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__chemical.temperature_sublimation
_definition.id '_chemical.temperature_sublimation'
loop_
_alias.definition_id
'_chemical.temperature_sublimation'
'_chemical_temperature_sublimation'
_definition.update 2012-12-11
_description.text
;
The temperature at which a crystalline solid sublimates.
;
_name.category_id chemical
_name.object_id temperature_sublimation
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__chemical.temperature_sublimation_gt
_definition.id '_chemical.temperature_sublimation_gt'
loop_
_alias.definition_id
'_chemical.temperature_sublimation_gt'
'_chemical_temperature_sublimation_gt'
_definition.update 2012-12-11
_description.text
;
The temperature above which a crystalline solid sublimates.
_chemical.temperature_sublimation should be used in preference.
;
_name.category_id chemical
_name.object_id temperature_sublimation_gt
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__chemical.temperature_sublimation_lt
_definition.id '_chemical.temperature_sublimation_lt'
loop_
_alias.definition_id
'_chemical.temperature_sublimation_lt'
'_chemical_temperature_sublimation_lt'
_definition.update 2012-12-11
_description.text
;
The temperature below which a crystalline solid sublimates.
_chemical.temperature_sublimation should be used in preference.
;
_name.category_id chemical
_name.object_id temperature_sublimation_lt
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__chemical.temperature_sublimation_su
_definition.id '_chemical.temperature_sublimation_su'
loop_
_alias.definition_id
'_chemical.temperature_sublimation_su'
'_chemical_temperature_sublimation_su'
'_chemical.temperature_sublimation_esd'
_definition.update 2012-12-11
_description.text
;
Standard Uncertainty of the
temperature at which a crystalline solid sublimates.
;
_name.category_id chemical
_name.object_id temperature_sublimation_su
_name.linked_item_id '_chemical.temperature_sublimation'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save_CHEMICAL_CONN_ATOM
_definition.id CHEMICAL_CONN_ATOM
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items which describe the 2D chemical structure of
the molecular species. They allow a 2D chemical diagram to be
reconstructed for use in a publication or in a database search
for structural and substructural relationships. In particular,
the chemical_conn_atom data items provide information about the
chemical properties of the atoms in the structure. In cases
where crystallographic and molecular symmetry elements coincide
they must also contain symmetry-generated atoms, so as to describe
a complete chemical entity.
;
_name.category_id CHEMICAL
_name.object_id CHEMICAL_CONN_ATOM
_category.key_id '_chemical_conn_atom.key'
_category.key_list ['_chemical_conn_atom.number']
save_
save__chemical_conn_atom.charge
_definition.id '_chemical_conn_atom.charge'
loop_
_alias.definition_id
'_chemical_conn_atom.charge'
'_chemical_conn_atom_charge'
_definition.update 2012-11-22
_description.text
;
The net integer charge assigned to this atom. This is the
formal charge assignment normally found in chemical diagrams.
;
_name.category_id chemical_conn_atom
_name.object_id charge
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Integer
_enumeration.range -6:6
_enumeration.default 0
save_
save__chemical_conn_atom.display_x
_definition.id '_chemical_conn_atom.display_x'
loop_
_alias.definition_id
'_chemical_conn_atom.display_x'
'_chemical_conn_atom_display_x'
_definition.update 2012-11-22
_description.text
;
Cartesian coordinate (x) of the atom site in a chemical diagram. The
coordinate origin is at the lower left corner, the x axis is horizontal.
;
_name.category_id chemical_conn_atom
_name.object_id display_x
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save__chemical_conn_atom.display_y
_definition.id '_chemical_conn_atom.display_y'
loop_
_alias.definition_id
'_chemical_conn_atom.display_y'
'_chemical_conn_atom_display_y'
_definition.update 2012-11-22
_description.text
;
Cartesian coordinate (y) of the atom site in a chemical diagram. The
coordinate origin is at the lower left corner, the y axis is vertical.
;
_name.category_id chemical_conn_atom
_name.object_id display_y
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save__chemical_conn_atom.key
_definition.id '_chemical_conn_atom.key'
loop_
_alias.definition_id
'_chemical_conn_atom.key'
_definition.update 2012-11-22
_description.text
;
Value is a unique key to a set of CHEMICAL_CONN_ATOM items
in a looped list.
;
_name.category_id chemical_conn_atom
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Index
loop_
_method.purpose
_method.expression
Evaluation ' _chemical_conn_atom.key = _chemical_conn_atom.number'
save_
save__chemical_conn_atom.NCA
_definition.id '_chemical_conn_atom.NCA'
loop_
_alias.definition_id
'_chemical_conn_atom.NCA'
'_chemical_conn_atom_NCA'
_definition.update 2012-11-22
_description.text
;
Total number of connected atoms excluding terminal hydrogen atoms.
;
_name.category_id chemical_conn_atom
_name.object_id NCA
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save__chemical_conn_atom.NH
_definition.id '_chemical_conn_atom.NH'
loop_
_alias.definition_id
'_chemical_conn_atom.NH'
'_chemical_conn_atom_NH'
_definition.update 2012-11-22
_description.text
;
Total number of hydrogen atoms attached to this atom,
regardless of whether they are included in the refinement or
the atom_site list. This number will be the same as
_atom_site.attached_hydrogens only if none of the hydrogen
atoms appear in the atom_site list.
;
_name.category_id chemical_conn_atom
_name.object_id NH
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save__chemical_conn_atom.number
_definition.id '_chemical_conn_atom.number'
loop_
_alias.definition_id
'_chemical_conn_atom.number'
'_chemical_conn_atom_number'
_definition.update 2012-11-22
_description.text
;
The chemical sequence number to be associated with this atom.
;
_name.category_id chemical_conn_atom
_name.object_id number
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Index
_enumeration.range 1:
save_
save__chemical_conn_atom.type_symbol
_definition.id '_chemical_conn_atom.type_symbol'
loop_
_alias.definition_id
'_chemical_conn_atom.type_symbol'
'_chemical_conn_atom_type_symbol'
_definition.update 2012-11-22
_description.text
;
A code identifying the atom type.
;
_name.category_id chemical_conn_atom
_name.object_id type_symbol
_name.linked_item_id '_atom_type.symbol'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save_CHEMICAL_CONN_BOND
_definition.id CHEMICAL_CONN_BOND
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items which specify the connections between
the atoms sites in the chemical_conn_atom list and the nature
of the chemical bond between these atoms. These are details about
the two-dimensional (2D) chemical structure of the molecular species.
They allow a 2D chemical diagram to be reconstructed for use in a
publication or in a database search for structural and substructural
relationships.
;
_name.category_id CHEMICAL
_name.object_id CHEMICAL_CONN_BOND
_category.key_id '_chemical_conn_bond.key'
_category.key_list ['_chemical_conn_bond.atom_1' '_chemical_conn_bond.atom_2']
save_
save__chemical_conn_bond.atom_1
_definition.id '_chemical_conn_bond.atom_1'
loop_
_alias.definition_id
'_chemical_conn_bond.atom_1'
'_chemical_conn_bond_atom_1'
'_chem_comp_bond.atom_id_1'
_definition.update 2012-11-22
_description.text
;
Index id of first atom in a bond connecting two atom sites.
;
_name.category_id chemical_conn_bond
_name.object_id atom_1
_name.linked_item_id '_chemical_conn_atom.number'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Index
_enumeration.range 1:
save_
save__chemical_conn_bond.atom_2
_definition.id '_chemical_conn_bond.atom_2'
loop_
_alias.definition_id
'_chemical_conn_bond.atom_2'
'_chemical_conn_bond_atom_2'
'_chem_comp_bond.atom_id_2'
_definition.update 2012-11-22
_description.text
;
Index id of second atom in a bond connecting two atom sites.
;
_name.category_id chemical_conn_bond
_name.linked_item_id '_chemical_conn_atom.number'
_name.object_id atom_2
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Index
_enumeration.range 1:
save_
save__chemical_conn_bond.distance
_definition.id '_chemical_conn_bond.distance'
loop_
_alias.definition_id
'_chemical_conn_bond.distance'
'_chem_comp_bond.value_dist'
_definition.update 2014-06-12
_description.text
;
The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a
distance.
;
_name.category_id chemical_conn_bond
_name.object_id distance
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.5:
_enumeration.default 0.0
_units.code angstroms
save_
save__chemical_conn_bond.distance_su
_definition.id '_chemical_conn_bond.distance_su'
loop_
_alias.definition_id
'_chemical_conn_bond.distance_su'
'_chem_comp_bond.value_dist_esd'
_definition.update 2014-06-12
_description.text
;
The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a
distance.
;
_name.category_id chemical_conn_bond
_name.object_id distance_su
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.5:
_enumeration.default 0.0
_units.code angstroms
save_
save__chemical_conn_bond.id
_definition.id '_chemical_conn_bond.id'
loop_
_alias.definition_id
'_chemical_conn_bond.id'
_definition.update 2012-11-22
_description.text
;
Bond identifier composed of a list of two sequence indices
specified as _chemical_conn_atom.number values.
;
_name.category_id chemical_conn_bond
_name.object_id id
_type.purpose Number
_type.source Derived
_type.container List
_type.contents Index
_type.dimension [2]
loop_
_method.purpose
_method.expression
Evaluation
;
With c as chemical_conn_bond
_chemical_conn_bond.id = [ c.atom_1, c.atom_2 ]
;
save_
save__chemical_conn_bond.key
_definition.id '_chemical_conn_bond.key'
loop_
_alias.definition_id
'_chemical_conn_bond.key'
_definition.update 2012-11-22
_description.text
;
Value is a unique key to a set of CHEMICAL_CONN_BOND items
in a looped list.
;
_name.category_id chemical_conn_bond
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Index
loop_
_method.purpose
_method.expression
Evaluation ' _chemical_conn_bond.key = _chemical_conn_bond.id'
save_
save__chemical_conn_bond.type
_definition.id '_chemical_conn_bond.type'
loop_
_alias.definition_id
'_chemical_conn_bond.type'
'_chemical_conn_bond_type'
'_chem_comp_bond.value_order'
_definition.update 2012-11-22
_description.text
;
Code for the chemical bond type.
;
_name.category_id chemical_conn_bond
_name.object_id type
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
sing 'single bond'
doub 'double bond'
trip 'triple bond'
quad 'quadruple bond'
arom 'aromatic bond'
poly 'polymeric bond'
delo 'delocalized double bond'
pi 'pi bond'
_enumeration.default sing
save_
save_CHEMICAL_FORMULA
_definition.id CHEMICAL_FORMULA
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items which specify the composition and chemical
properties of the compound. The formula data items must agree
with those that specify the density, unit-cell and Z values.
The following rules apply to the construction of the data items
_chemical_formula.analytical, *.structural and *.sum. For the
data item *.moiety the formula construction is broken up into
residues or moieties, i.e. groups of atoms that form a molecular
unit or molecular ion. The rules given below apply within each
moiety but different requirements apply to the way that moieties
are connected (see _chemical_formula.moiety).
1. Only recognized element symbols may be used.
2. Each element symbol is followed by a 'count' number. A count of
'1' may be omitted.
3. A space or parenthesis must separate each cluster of (element
symbol + count).
4. Where a group of elements is enclosed in parentheses, the
multiplier for the group must follow the closing parentheses.
That is, all element and group multipliers are assumed to be
printed as subscripted numbers. [An exception to this rule
exists for *.moiety formulae where pre- and post-multipliers
are permitted for molecular units].
5. Unless the elements are ordered in a manner that corresponds to
their chemical structure, as in _chemical_formula.structural,
the order of the elements within any group or moiety
depends on whether or not carbon is present. If carbon is
present, the order should be: C, then H, then the other
elements in alphabetical order of their symbol. If carbon is
not present, the elements are listed purely in alphabetic order
of their symbol. This is the 'Hill' system used by Chemical
Abstracts. This ordering is used in _chemical_formula.moiety
and _chemical_formula.sum.
_chemical_formula.iupac '[Mo (C O)4 (C18 H33 P)2]'
_chemical_formula.moiety 'C40 H66 Mo O4 P2'
_chemical_formula.structural '((C O)4 (P (C6 H11)3)2)Mo'
_chemical_formula.sum 'C40 H66 Mo O4 P2'
_chemical_formula.weight 768.81
;
_name.category_id CHEMICAL
_name.object_id CHEMICAL_FORMULA
save_
save__chemical_formula.analytical
_definition.id '_chemical_formula.analytical'
loop_
_alias.definition_id
'_chemical_formula.analytical'
'_chemical_formula_analytical'
_definition.update 2012-11-22
_description.text
;
Formula determined by standard chemical analysis including trace
elements. Parentheses are used only for standard uncertainties (su's).
;
_name.category_id chemical_formula
_name.object_id analytical
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Text
loop_
_description_example.case
'Fe2.45(2) Ni1.60(3) S4'
save_
save__chemical_formula.iupac
_definition.id '_chemical_formula.iupac'
loop_
_alias.definition_id
'_chemical_formula.iupac'
'_chemical_formula_iupac'
_definition.update 2012-11-22
_description.text
;
Formula expressed in conformance with IUPAC rules for inorganic
and metal-organic compounds where these conflict with the rules
for any other chemical_formula entries. Typically used for
formatting a formula in accordance with journal rules. This
should appear in the data block in addition to the most
appropriate of the other chemical_formula data names.
Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry.
Oxford: Blackwell Scientific Publications.
;
_name.category_id chemical_formula
_name.object_id iupac
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Text
loop_
_description_example.case
'[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H'
save_
save__chemical_formula.moiety
_definition.id '_chemical_formula.moiety'
loop_
_alias.definition_id
'_chemical_formula.moiety'
'_chemical_formula_moiety'
_definition.update 2012-11-22
_description.text
;
Formula with each discrete bonded residue or ion shown as a
separate moiety. See above CHEMICAL_FORMULA for rules
for writing chemical formulae. In addition to the general
formulae requirements, the following rules apply:
1. Moieties are separated by commas ','.
2. The order of elements within a moiety follows general rule
5 in CHEMICAL_FORMULA.
3. Parentheses are not used within moieties but may surround
a moiety. Parentheses may not be nested.
4. Charges should be placed at the end of the moiety. The
Singlege '+' or '-' may be preceded by a numerical multiplier
and should be separated from the last (element symbol +
count) by a space. Pre- or post-multipliers may be used for
individual moieties.
;
_name.category_id chemical_formula
_name.object_id moiety
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Text
loop_
_description_example.case
'C7 H4 Cl Hg N O3 S'
'C12 H17 N4 O S 1+, C6 H2 N3 O7 1-'
'C12 H16 N2 O6, 5(H2 O1)'
'(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O)'
save_
save__chemical_formula.structural
_definition.id '_chemical_formula.structural'
loop_
_alias.definition_id
'_chemical_formula.structural'
'_chemical_formula_structural'
_definition.update 2012-11-22
_description.text
;
This formula should correspond to the structure as reported, i.e.
trace elements not included in atom type and atom site lists should
not be included. See category description for the rules for writing
chemical formulae for inorganics, organometallics, metal complexes
etc., in which bonded groups are preserved as discrete entities
within parentheses, with post-multipliers as required. The order of
the elements should give as much information as possible about the
chemical structure. Parentheses may be used and nested as required.
This formula should correspond to the structure as actually reported,
i.e. trace elements not included in atom-type and atom-site lists
should not be included (see also _chemical_formula.analytical).
;
_name.category_id chemical_formula
_name.object_id structural
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Text
loop_
_description_example.case
'(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2'
'Ca ((Cl O3)2 O)2 (H2 O)6'
save_
save__chemical_formula.sum
_definition.id '_chemical_formula.sum'
loop_
_alias.definition_id
'_chemical_formula.sum'
'_chemical_formula_sum'
_definition.update 2012-11-22
_description.text
;
Chemical formulae in which all discrete bonded residues and ions are
summed over the constituent elements, following the ordering given
in rule 5 of the CATEGORY description. Parentheses normally not used.
;
_name.category_id chemical_formula
_name.object_id sum
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Text
loop_
_description_example.case
'C18 H19 N7 O8 S'
save_
save__chemical_formula.weight
_definition.id '_chemical_formula.weight'
loop_
_alias.definition_id
'_chemical_formula.weight'
'_chemical_formula_weight'
_definition.update 2012-11-22
_description.text
;
Mass corresponding to the formulae _chemical_formula.structural,
*_iupac, *_moiety or *_sum and, together with the Z value and cell
parameters yield the density given as _exptl_crystal.density_diffrn.
;
_name.category_id chemical_formula
_name.object_id weight
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 1.0:
_units.code dalton
save_
save__chemical_formula.weight_meas
_definition.id '_chemical_formula.weight_meas'
loop_
_alias.definition_id
'_chemical_formula.weight_meas'
'_chemical_formula_weight_meas'
_definition.update 2012-11-22
_description.text
;
Formula mass measured by a non-diffraction experiment.
;
_name.category_id chemical_formula
_name.object_id weight_meas
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 1.0:
_units.code dalton
save_
save_EXPTL_CRYSTALS
_definition.id EXPTL_CRYSTALS
_definition.scope Category
_definition.class Ref-loop
_definition.update 2013-09-08
_description.text
;
This category is designed specifically to facilitate studies
involving multiple sets of experiments and their associated data
values. The data items are defined in the EXPTL_CRYSTAL category.
This category class is only used in an instance document when
there is more than one experiment encompassed by the category of
EXPTL items. When this is the case each set of EXPTL_CRYSTALa
data, one set per experiment, is enclosed in its own save frame.
In the instance document these are referred to as a loop of
the item _experiments.key. See a typical example below.
When only one set of experimental data exists the EXPTL items
need not be enclosed in a save frame and the reference loop is
unnecessary.
;
_name.category_id EXPTL
_name.object_id EXPTL_CRYSTALS
_category.key_id '_exptl_crystals.key'
_category.key_list ['_exptl_crystals.key']
loop_
_description_example.case
;
In an instance document this category is typically invoked as
loop_ _exptl_crystals.key
${"frame":"crystal_1"}$
${"frame":"crystal_2"}$
;
save_
save__exptl_crystals.key
_definition.id '_exptl_crystals.key'
loop_
_alias.definition_id
'_exptl_crystals.key'
_definition.update 2012-11-22
_description.text
;
Unique key code to a set of EXPTL_CRYSTAL items in a looped list.
;
_name.category_id exptl_crystals
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Ref-table
_type.contents Code
loop_
_description_example.case
' ${"frame":c1}$ '
save_
save_EXPTL_ABSORPT
_definition.id EXPTL_ABSORPT
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items used to specify the experimental details
of the absorption measurements and corrections to the diffraction
data.
;
_name.category_id EXPTL_CRYSTALS
_name.object_id EXPTL_ABSORPT
save_
save__exptl_absorpt.coefficient_mu
_definition.id '_exptl_absorpt.coefficient_mu'
loop_
_alias.definition_id
'_exptl_absorpt.coefficient_mu'
'_exptl_absorpt_coefficient_mu'
'_exptl.absorpt_coefficient_mu'
_definition.update 2012-11-22
_description.text
;
Absorption coefficient mu calculated from the atomic content of
the cell, the density and the radiation wavelength.
;
_name.category_id exptl_absorpt
_name.object_id coefficient_mu
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code reciprocal_millimetres
save_
save__exptl_absorpt.correction_T_max
_definition.id '_exptl_absorpt.correction_T_max'
loop_
_alias.definition_id
'_exptl_absorpt.correction_T_max'
'_exptl_absorpt_correction_T_max'
'_exptl.absorpt_correction_T_max'
_definition.update 2012-11-22
_description.text
;
Maximum transmission factor for the crystal and radiation applied
to the measured intensities, it includes the correction for
absorption by the specimen mount and diffractometer as well
as by the specimen itself. These values give the transmission (T)
factor by which measured intensities have been REDUCED due to
absorption. Sometimes referred to as absorption correction A or
1/A* (see "Crystal Structure Analysis for Chemists and Biologists"
by J.P. Glusker et al., Wiley)
;
_name.category_id exptl_absorpt
_name.object_id correction_T_max
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save__exptl_absorpt.correction_T_min
_definition.id '_exptl_absorpt.correction_T_min'
loop_
_alias.definition_id
'_exptl_absorpt.correction_T_min'
'_exptl_absorpt_correction_T_min'
'_exptl.absorpt_correction_T_min'
_definition.update 2012-11-22
_description.text
;
Maximum transmission factor for the crystal and radiation applied
to the measured intensities, it includes the correction for
absorption by the specimen mount and diffractometer as well
as by the specimen itself. These values give the transmission (T)
factor by which measured intensities have been REDUCED due to
absorption. Sometimes referred to as absorption correction A ori
1/A* (see "Crystal Structure Analysis for Chemists and Biologists"
by J.P. Glusker et al., Wiley)
;
_name.category_id exptl_absorpt
_name.object_id correction_T_min
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save__exptl_absorpt.correction_type
_definition.id '_exptl_absorpt.correction_type'
loop_
_alias.definition_id
'_exptl_absorpt.correction_type'
'_exptl_absorpt_correction_type'
'_exptl.absorpt_correction_type'
_definition.update 2012-11-22
_description.text
;
Code identifying the absorption correction type and method.
The 'empirical' approach should NOT be used if more detailed
information on the crystal shape is available.
;
_name.category_id exptl_absorpt
_name.object_id correction_type
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
analytical 'analytical from crystal shape'
cylinder cylindrical
empirical 'empirical from intensities'
gaussian 'Gaussian from crystal shape'
integration 'integration from crystal shape'
multi-scan 'symmetry-related measurements'
none 'no absorption correction applied'
numerical 'numerical from crystal shape'
psi-scan 'psi-scan corrections'
refdelf 'refined from delta-F'
sphere spherical
_enumeration.default none
save_
save__exptl_absorpt.process_details
_definition.id '_exptl_absorpt.process_details'
loop_
_alias.definition_id
'_exptl_absorpt.process_details'
'_exptl_absorpt_process_details'
'_exptl.absorpt_process_details'
_definition.update 2012-11-22
_description.text
;
Description of the absorption correction process applied to the
measured intensities. A literature reference should be supplied
for psi-scan or multi-scan techniques.
;
_name.category_id exptl_absorpt
_name.object_id process_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'Tompa analytical'
'MolEN (Fair, 1990)'
'(North, Phillips & Mathews, 1968)'
save_
save_EXPTL_CRYSTAL
_definition.id EXPTL_CRYSTAL
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items used to specify information about a
crystal used in the diffraction measurements.
;
_name.category_id EXPTL_CRYSTALS
_name.object_id EXPTL_CRYSTAL
save_
save__exptl_crystal.colour
_definition.id '_exptl_crystal.colour'
loop_
_alias.definition_id
'_exptl_crystal.colour'
'_exptl_crystal_colour'
_definition.update 2012-11-22
_description.text
;
Colour description of a crystal as a list of the allowed
exptl_crystal_appearance states for general, intensity and hue.
;
_name.category_id exptl_crystal
_name.object_id colour
_type.purpose Composite
_type.source Derived
_type.container List
_type.contents Code
_type.dimension [3]
loop_
_description_example.case
'[transluscent, pale, green]'
loop_
_method.purpose
_method.expression
Evaluation
;
With c as exptl_crystal_appearance
_exptl_crystal.colour = [ c.general, c.intensity, c.hue ]
;
save_
save__exptl_crystal.density_diffrn
_definition.id '_exptl_crystal.density_diffrn'
loop_
_alias.definition_id
'_exptl_crystal.density_diffrn'
'_exptl_crystal_density_diffrn'
_definition.update 2012-11-22
_description.text
;
Crystal density calculated from crystal unit cell and atomic content.
;
_name.category_id exptl_crystal
_name.object_id density_diffrn
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code megagrams_per_metre_cubed
loop_
_method.purpose
_method.expression
Evaluation
;
_exptl_crystal.density_diffrn = 1.6605 * _cell.atomic_mass / _cell.volume
;
save_
save__exptl_crystal.density_meas
_definition.id '_exptl_crystal.density_meas'
loop_
_alias.definition_id
'_exptl_crystal.density_meas'
'_exptl_crystal_density_meas'
_definition.update 2012-11-22
_description.text
;
Crystal density measured using standard chemical and physical methods.
;
_name.category_id exptl_crystal
_name.object_id density_meas
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code megagrams_per_metre_cubed
save_
save__exptl_crystal.density_meas_gt
_definition.id '_exptl_crystal.density_meas_gt'
loop_
_alias.definition_id
'_exptl_crystal.density_meas_gt'
'_exptl_crystal_density_meas_gt'
_definition.update 2012-12-11
_description.text
;
The value above which the density measured using standard
chemical and physical methods lies. This item is used only
when _exptl_crystal.density_meas cannot be employed. It is
intended for use in reporting information in databases and
archives which would be misleading if reported otherwise.
;
_name.category_id exptl_crystal
_name.object_id density_meas_gt
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code megagrams_per_metre_cubed
save_
save__exptl_crystal.density_meas_lt
_definition.id '_exptl_crystal.density_meas_lt'
loop_
_alias.definition_id
'_exptl_crystal.density_meas_lt'
'_exptl_crystal_density_meas_lt'
_definition.update 2012-12-11
_description.text
;
The value below which the density measured using standard
chemical and physical methods lies. This item is used only
when _exptl_crystal.density_meas cannot be employed. It is
intended for use in reporting information in databases and
archives which would be misleading if reported otherwise.
;
_name.category_id exptl_crystal
_name.object_id density_meas_lt
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code megagrams_per_metre_cubed
save_
save__exptl_crystal.density_meas_su
_definition.id '_exptl_crystal.density_meas_su'
loop_
_alias.definition_id
'_exptl_crystal.density_meas_su'
'_exptl_crystal_density_meas_su'
'_exptl_crystal.density_meas_esd'
_definition.update 2012-11-22
_description.text
;
Standard Uncertainty of the
Crystal density measured using standard chemical and physical methods.
;
_name.category_id exptl_crystal
_name.object_id density_meas_su
_name.linked_item_id '_exptl_crystal.density_meas'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code megagrams_per_metre_cubed
save_
save__exptl_crystal.density_meas_temp
_definition.id '_exptl_crystal.density_meas_temp'
loop_
_alias.definition_id
'_exptl_crystal.density_meas_temp'
'_exptl_crystal_density_meas_temp'
_definition.update 2012-11-22
_description.text
;
Temperature at which _exptl_crystal.density_meas was determined.
;
_name.category_id exptl_crystal
_name.object_id density_meas_temp
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_enumeration.default 293.
_units.code kelvins
save_
save__exptl_crystal.density_meas_temp_gt
_definition.id '_exptl_crystal.density_meas_temp_gt'
loop_
_alias.definition_id
'_exptl_crystal.density_meas_temp_gt'
'_exptl_crystal_density_meas_temp_gt'
_definition.update 2012-12-11
_description.text
;
Temperature above which the measured density was determined.
This item is used only when exptl_crystal.density_meas_temp
cannot be employed. It is intended for use in reporting values
from databases which would be misleading if reported otherwise.
;
_name.category_id exptl_crystal
_name.object_id density_meas_temp_gt
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_enumeration.default 293.
_units.code kelvins
save_
save__exptl_crystal.density_meas_temp_lt
_definition.id '_exptl_crystal.density_meas_temp_lt'
loop_
_alias.definition_id
'_exptl_crystal.density_meas_temp_lt'
'_exptl_crystal_density_meas_temp_lt'
_definition.update 2012-12-11
_description.text
;
Temperature below which the measured density was determined.
This item is used only when exptl_crystal.density_meas_temp
cannot be employed. It is intended for use in reporting values
from databases which would be misleading if reported otherwise.
;
_name.category_id exptl_crystal
_name.object_id density_meas_temp_lt
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_enumeration.default 293.
_units.code kelvins
save_
save__exptl_crystal.density_meas_temp_su
_definition.id '_exptl_crystal.density_meas_temp_su'
loop_
_alias.definition_id
'_exptl_crystal.density_meas_temp_su'
'_exptl_crystal_density_meas_temp_su'
'_exptl_crystal.density_meas_temp_esd'
_definition.update 2012-11-22
_description.text
;
Standard Uncertainty of the
Temperature at which _exptl_crystal.density_meas was determined.
;
_name.category_id exptl_crystal
_name.object_id density_meas_temp_su
_name.linked_item_id '_exptl_crystal.density_meas_temp'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code kelvins
save_
save__exptl_crystal.density_method
_definition.id '_exptl_crystal.density_method'
loop_
_alias.definition_id
'_exptl_crystal.density_method'
'_exptl_crystal_density_method'
_definition.update 2012-11-22
_description.text
;
Description of method used to measure _exptl_crystal.density_meas.
;
_name.category_id exptl_crystal
_name.object_id density_method
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'flotation in aqueous KI'
save_
save__exptl_crystal.description
_definition.id '_exptl_crystal.description'
loop_
_alias.definition_id
'_exptl_crystal.description'
'_exptl_crystal_description'
_definition.update 2012-11-22
_description.text
;
Description of the quality and habit of the crystal. The crystal
dimensions should appear in the exptl_crystal_size category.
;
_name.category_id exptl_crystal
_name.object_id description
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__exptl_crystal.F_000
_definition.id '_exptl_crystal.F_000'
loop_
_alias.definition_id
'_exptl_crystal.F_000'
'_exptl_crystal_F_000'
_definition.update 2012-11-22
_description.text
;
Number of electrons in the crystal unit cell contributing to F(000).
It may contain dispersion contributions, and is calculated as
F(000) = [ (sum f~r~)^2^ + (sum f~i~)^2^ ]^1/2^
f~r~ = real part of the scattering factors at theta = 0
f~i~ = imaginary part of the scattering factors at theta = 0
the sum is taken over each atom in the unit cell
For X-rays, non-dispersive F(000) is a positive number and counts
the effective number of electrons in the unit cell; for neutrons,
non-dispersive F(000) (which may be negative) counts the total
nuclear scattering power in the unit cell. See
http://reference.iucr.org/dictionary/F(000)
;
_name.category_id exptl_crystal
_name.object_id F_000
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
loop_
_method.purpose
_method.expression
Definition
;
If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres"
Else If (_diffrn_radiation.probe == "electron") _units.code = "volts"
Else _units.code = "electrons"
;
save_
save__exptl_crystal.id
_definition.id '_exptl_crystal.id'
loop_
_alias.definition_id
'_exptl_crystal.id'
'_exptl_crystal_id'
_definition.update 2012-11-22
_description.text
;
Code identifying a crystal if multiple crystals are used.
See _exptl_crystals.key.
;
_name.category_id exptl_crystal
_name.object_id id
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__exptl_crystal.preparation
_definition.id '_exptl_crystal.preparation'
loop_
_alias.definition_id
'_exptl_crystal.preparation'
'_exptl_crystal_preparation'
_definition.update 2012-11-22
_description.text
;
Details of crystal growth and preparation of the crystals
(e.g. mounting) prior to the intensity measurements.
;
_name.category_id exptl_crystal
_name.object_id preparation
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'mounted in an argon-filled quartz capillary'
save_
save__exptl_crystal.pressure_history
_definition.id '_exptl_crystal.pressure_history'
loop_
_alias.definition_id
'_exptl_crystal.pressure_history'
'_exptl_crystal_pressure_history'
_definition.update 2012-11-22
_description.text
;
Details concerning the pressure history of the crystals.
;
_name.category_id exptl_crystal
_name.object_id pressure_history
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__exptl_crystal.recrystallization_method
_definition.id '_exptl_crystal.recrystallization_method'
loop_
_alias.definition_id
'_exptl_crystal.recrystallization_method'
'_exptl_crystal_recrystallization_method'
_definition.update 2012-12-11
_description.text
;
Method used to recrystallize the sample. Sufficient details should
be given for the procedure to be repeated. Temperatures, solvents,
flux or carrier gases with concentrations or pressures and ambient
atmosphere details should be given.
;
_name.category_id exptl_crystal
_name.object_id recrystallization_method
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__exptl_crystal.size_length
_definition.id '_exptl_crystal.size_length'
loop_
_alias.definition_id
'_exptl_crystal.size_length'
'_exptl_crystal_size_length'
_definition.update 2012-11-22
_description.text
;
The length of needle/cylindrical crystals.
;
_name.category_id exptl_crystal
_name.object_id size_length
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code millimetres
save_
save__exptl_crystal.size_max
_definition.id '_exptl_crystal.size_max'
loop_
_alias.definition_id
'_exptl_crystal.size_max'
'_exptl_crystal_size_max'
_definition.update 2012-11-22
_description.text
;
The maximum dimension of a crystal.
;
_name.category_id exptl_crystal
_name.object_id size_max
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code millimetres
save_
save__exptl_crystal.size_mid
_definition.id '_exptl_crystal.size_mid'
loop_
_alias.definition_id
'_exptl_crystal.size_mid'
'_exptl_crystal_size_mid'
_definition.update 2012-11-22
_description.text
;
The median dimension of a crystal.
;
_name.category_id exptl_crystal
_name.object_id size_mid
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code millimetres
save_
save__exptl_crystal.size_min
_definition.id '_exptl_crystal.size_min'
loop_
_alias.definition_id
'_exptl_crystal.size_min'
'_exptl_crystal_size_min'
_definition.update 2012-11-22
_description.text
;
The minimum dimension of a crystal.
;
_name.category_id exptl_crystal
_name.object_id size_min
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code millimetres
save_
save__exptl_crystal.size_rad
_definition.id '_exptl_crystal.size_rad'
loop_
_alias.definition_id
'_exptl_crystal.size_rad'
'_exptl_crystal_size_rad'
_definition.update 2012-11-22
_description.text
;
The radius of a spherical or cylindrical crystal.
;
_name.category_id exptl_crystal
_name.object_id size_rad
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code millimetres
save_
save__exptl_crystal.thermal_history
_definition.id '_exptl_crystal.thermal_history'
loop_
_alias.definition_id
'_exptl_crystal.thermal_history'
'_exptl_crystal_thermal_history'
_definition.update 2012-11-22
_description.text
;
Details concerning the thermal history of the crystals.
;
_name.category_id exptl_crystal
_name.object_id thermal_history
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_EXPTL_CRYSTAL_APPEARANCE
_definition.id EXPTL_CRYSTAL_APPEARANCE
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of ENUMERATION items used to specify information about the
crystal colour and appearance.
;
_name.category_id EXPTL_CRYSTAL
_name.object_id EXPTL_CRYSTAL_APPEARANCE
save_
save__exptl_crystal_appearance.general
_definition.id '_exptl_crystal_appearance.general'
loop_
_alias.definition_id
'_exptl_crystal_appearance.general'
'_exptl_crystal_colour_lustre'
'_exptl_crystal.colour_lustre'
_definition.update 2012-11-22
_description.text
;
Appearance of the crystal as prescribed state codes.
;
_name.category_id exptl_crystal_appearance
_name.object_id general
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
metallic
lustrous
transparent
transluscent
opaque
.
_enumeration.default .
save_
save__exptl_crystal_appearance.hue
_definition.id '_exptl_crystal_appearance.hue'
loop_
_alias.definition_id
'_exptl_crystal_appearance.hue'
'_exptl_crystal_colour_primary'
'_exptl_crystal.colour_primary'
_definition.update 2012-11-22
_description.text
;
Colour hue of the crystals as prescribed state codes.
;
_name.category_id exptl_crystal_appearance
_name.object_id hue
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
_enumeration.default white
loop_
_enumeration_set.state
_enumeration_set.detail
black '[ 000, 000, 000 ]'
white '[ 255, 255, 255 ]'
grey '[ 192, 192, 192 ]'
grey_light '[ 211, 211, 211 ]'
grey_slate '[ 112, 128, 144 ]'
blue '[ 000, 000, 255 ]'
blue_light '[ 176, 224, 230 ]'
blue_medium '[ 000, 000, 205 ]'
blue_dark '[ 025, 025, 112 ]'
blue_navy '[ 000, 000, 128 ]'
blue_royal '[ 065, 105, 225 ]'
blue_sky '[ 135, 206, 235 ]'
blue_steel '[ 070, 130, 180 ]'
turquoise '[ 064, 224, 208 ]'
cyan '[ 000, 255, 255 ]'
cyan_light '[ 224, 255, 255 ]'
green '[ 000, 255, 000 ]'
green_light '[ 152, 251, 152 ]'
green_dark '[ 000, 100, 000 ]'
green_sea '[ 046, 139, 087 ]'
green_lime '[ 050, 205, 050 ]'
green_olive '[ 107, 142, 035 ]'
green_khaki '[ 240, 230, 140 ]'
yellow '[ 255, 255, 000 ]'
yellow_light '[ 255, 255, 224 ]'
yellow_gold '[ 255, 215, 000 ]'
brown '[ 165, 042, 042 ]'
brown_sienna '[ 160, 082, 045 ]'
brown_beige '[ 245, 245, 220 ]'
brown_tan '[ 210, 180, 140 ]'
salmon '[ 250, 128, 114 ]'
salmon_light '[ 255, 160, 122 ]'
salmon_dark '[ 233, 150, 122 ]'
orange '[ 255, 165, 000 ]'
orange_dark '[ 255, 140, 000 ]'
red '[ 255, 000, 000 ]'
red_coral '[ 255, 127, 080 ]'
red_tomato '[ 255, 099, 071 ]'
red_orange '[ 255, 069, 000 ]'
red_violet '[ 219, 112, 147 ]'
red_maroon '[ 176, 048, 096 ]'
pink '[ 255, 192, 203 ]'
pink_light '[ 255, 182, 193 ]'
pink_deep '[ 255, 020, 147 ]'
pink_hot '[ 255, 105, 180 ]'
violet '[ 238, 130, 238 ]'
violet_red '[ 208, 032, 144 ]'
violet_magenta '[ 255, 000, 255 ]'
violet_dark '[ 148, 000, 211 ]'
violet_blue '[ 138, 043, 226 ]'
save_
save__exptl_crystal_appearance.intensity
_definition.id '_exptl_crystal_appearance.intensity'
loop_
_alias.definition_id
'_exptl_crystal_appearance.intensity'
'_exptl_crystal_colour_modifier'
'_exptl_crystal.colour_modifier'
_definition.update 2012-11-22
_description.text
;
Colour intensity of the crystal as prescribed state codes.
;
_name.category_id exptl_crystal_appearance
_name.object_id intensity
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
dark
light
intense
pale
whitish
blackish
grayish
brownish
reddish
pinkish
orangish
yellowish
greenish
bluish
.
_enumeration.default .
save_
save_EXPTL_CRYSTAL_FACE
_definition.id EXPTL_CRYSTAL_FACE
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items which specify the dimensions of the
crystals used in the diffraction measurements.
;
_name.category_id EXPTL_CRYSTAL
_name.object_id EXPTL_CRYSTAL_FACE
_category.key_id '_exptl_crystal_face.key'
_category.key_list ['_exptl_crystal_face.id']
save_
save__exptl_crystal_face.crystal_id
_definition.id '_exptl_crystal_face.crystal_id'
loop_
_alias.definition_id
'_exptl_crystal_face.crystal_id'
_definition.update 2012-11-22
_description.text
;
Code identifying a crystal if multiple crystals are used.
;
_name.category_id exptl_crystal_face
_name.object_id crystal_id
_name.linked_item_id '_exptl_crystal.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save__exptl_crystal_face.diffr_chi
_definition.id '_exptl_crystal_face.diffr_chi'
loop_
_alias.definition_id
'_exptl_crystal_face.diffr_chi'
'_exptl_crystal_face_diffr_chi'
_name.category_id exptl_crystal_face
_name.object_id diffr_chi
_type.contents Real
_type.purpose Measurand
_description.text
;
Diffractometer angle setting when the perpendicular to the specified
crystal face is aligned along a specified direction (e.g. the
bisector of the incident and reflected beams in an optical goniometer.
;
_enumeration.range -180.:180.
_type.source Recorded
_type.container Single
_definition.update 2013-04-15
_units.code degrees
save_
save__exptl_crystal_face.diffr_kappa
_definition.id '_exptl_crystal_face.diffr_kappa'
loop_
_alias.definition_id
'_exptl_crystal_face.diffr_kappa'
'_exptl_crystal_face_diffr_kappa'
_name.category_id exptl_crystal_face
_name.object_id diffr_kappa
_type.contents Real
_type.purpose Measurand
_description.text
;
Diffractometer angle setting when the perpendicular to the specified
crystal face is aligned along a specified direction (e.g. the
bisector of the incident and reflected beams in an optical goniometer.
;
_enumeration.range -180.:180.
_type.source Recorded
_type.container Single
_definition.update 2013-04-15
_units.code degrees
save_
save__exptl_crystal_face.diffr_phi
_definition.id '_exptl_crystal_face.diffr_phi'
loop_
_alias.definition_id
'_exptl_crystal_face.diffr_phi'
'_exptl_crystal_face_diffr_phi'
_name.category_id exptl_crystal_face
_name.object_id diffr_phi
_type.contents Real
_type.purpose Measurand
_description.text
;
Diffractometer angle setting when the perpendicular to the specified
crystal face is aligned along a specified direction (e.g. the
bisector of the incident and reflected beams in an optical goniometer.
;
_enumeration.range -180.:180.
_type.source Recorded
_type.container Single
_definition.update 2013-04-15
_units.code degrees
save_
save__exptl_crystal_face.diffr_psi
_definition.id '_exptl_crystal_face.diffr_psi'
loop_
_alias.definition_id
'_exptl_crystal_face.diffr_psi'
'_exptl_crystal_face_diffr_psi'
_name.category_id exptl_crystal_face
_name.object_id diffr_psi
_type.contents Real
_type.purpose Measurand
_description.text
;
Diffractometer angle setting when the perpendicular to the specified
crystal face is aligned along a specified direction (e.g. the
bisector of the incident and reflected beams in an optical goniometer.
;
_enumeration.range -180.:180.
_type.source Recorded
_type.container Single
_definition.update 2013-04-15
_units.code degrees
save_
save__exptl_crystal_face.hkl
_definition.id '_exptl_crystal_face.hkl'
loop_
_alias.definition_id
'_exptl_crystal_face.hkl'
_definition.update 2012-11-22
_description.text
;
Miller indices of the crystal face.
;
_name.category_id exptl_crystal_face
_name.object_id hkl
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Integer
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With f as exptl_crystal_face
_exptl_crystal_face.hkl = [f.index_h, f.index_h, f.index_l]
;
save_
save__exptl_crystal_face.id
_definition.id '_exptl_crystal_face.id'
loop_
_alias.definition_id
'_exptl_crystal_face.id'
_definition.update 2013-04-18
_description.text
;
Identifier which combines the crystal id and the face indices
as a list. This is normally the key item of the category.
;
_name.category_id exptl_crystal_face
_name.object_id id
_type.purpose Composite
_type.source Derived
_type.container List
_type.contents 'Code,Matrix(Index,Index,index)'
_type.dimension [1]
loop_
_method.purpose
_method.expression
Evaluation
;
With f as exptl_crystal_face
_exptl_crystal_face.id = [ f.crystal_id, f.hkl ]
;
save_
save__exptl_crystal_face.index_h
_definition.id '_exptl_crystal_face.index_h'
loop_
_alias.definition_id
'_exptl_crystal_face.index_h'
'_exptl_crystal_face_index_h'
_name.category_id exptl_crystal_face
_name.object_id index_h
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__exptl_crystal_face.index_k
_definition.id '_exptl_crystal_face.index_k'
loop_
_alias.definition_id
'_exptl_crystal_face.index_k'
'_exptl_crystal_face_index_k'
_name.category_id exptl_crystal_face
_name.object_id index_k
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__exptl_crystal_face.index_l
_definition.id '_exptl_crystal_face.index_l'
loop_
_alias.definition_id
'_exptl_crystal_face.index_l'
'_exptl_crystal_face_index_l'
_name.category_id exptl_crystal_face
_name.object_id index_l
_type.contents Integer
_type.purpose Number
_description.text
;
The index of a reciprocal space vector.
;
_enumeration.range -1000:1000
_type.source Recorded
_type.container Single
_definition.update 2013-04-16
_units.code none
save_
save__exptl_crystal_face.key
_definition.id '_exptl_crystal_face.key'
loop_
_alias.definition_id
'_exptl_crystal_face.key'
_definition.update 2012-11-22
_description.text
;
Value is a unique key to a set of EXPTL_CRYSTAL items
in a looped list.
;
_name.category_id exptl_crystal_face
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents 'Code,Matrix(Index,Index,index)'
loop_
_method.purpose
_method.expression
Evaluation ' _exptl_crystal_face.key = _exptl_crystal_face.id'
save_
save__exptl_crystal_face.perp_dist
_definition.id '_exptl_crystal_face.perp_dist'
loop_
_alias.definition_id
'_exptl_crystal_face.perp_dist'
'_exptl_crystal_face_perp_dist'
_definition.update 2012-11-22
_description.text
;
Perpendicular distance of face to the centre of rotation of the crystal.
;
_name.category_id exptl_crystal_face
_name.object_id perp_dist
_type.purpose Measurand
_type.source Recorded
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code millimetres
save_
save_SPACE_GROUPS
_definition.id SPACE_GROUPS
_definition.scope Category
_definition.class Ref-loop
_definition.update 2013-09-08
_description.text
;
Contains all the data items that refer to the space group as a
whole, such as its name, crystal system etc. It may be looped,
for example, in a list of space groups and their properties.
Only a subset of the SPACE_GROUP category items appear in the
core dictionary. The remainder are found in the cif_sym
dictionary.
Space group types are identified by their International Tables
for Crystallography Vol. A number. Specific settings of the
space groups can be identified either by their Hall symbol
or by specifying their symmetry operations.
The commonly-used Hermann-Mauguin symbol determines the
space group type uniquely but several different Hermann-Mauguin
symbols may refer to the same space group type. It contains
information on the choice of the basis, but not on the
choice of origin. Different formats for the Hermann-Mauguin
symbol are found in the cif_sym dictionary.
;
_name.category_id EXPTL
_name.object_id SPACE_GROUPS
_category.key_id '_space_groups.key'
_category.key_list ['_space_groups.key']
loop_
_description_example.case
;
In an instance document this category is typically invoked as
loop_ _exptl_crystals.key
${"frame":"space_group_1"}$
${"frame":"space_group_2"}$
;
save_
save__space_groups.key
_definition.id '_space_groups.key'
loop_
_alias.definition_id
'_space_groups.key'
_definition.update 2012-11-22
_description.text
;
Unique key code to a set of SPACE_GROUP items in a looped list.
;
_name.category_id space_groups
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Ref-table
_type.contents Code
loop_
_description_example.case
' ${"frame":"sg_set_1}$ '
save_
save_SPACE_GROUP
_definition.id SPACE_GROUP
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items used to specify space group
information about the crystal used in the diffraction measurements.
;
_name.category_id SPACE_GROUPS
_name.object_id SPACE_GROUP
save_
save__space_group.crystal_system
_definition.id '_space_group.crystal_system'
loop_
_alias.definition_id
'_space_group.crystal_system'
_definition.update 2014-06-12
_description.text
;
The name of the system of geometric crystal classes of space
groups (crystal system) to which the space group belongs.
Note that rhombohedral space groups belong to the
trigonal system.
;
_name.category_id space_group
_name.object_id crystal_system
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
triclinic
monoclinic
orthorhombic
tetragonal
trigonal
hexagonal
cubic
_enumeration.default triclinic
save_
save__space_group.id
_definition.id '_space_group.id'
loop_
_alias.definition_id
'_space_group.id'
'_space_group_id'
_definition.update 2012-11-22
_description.text
;
Code identifying a space group if multiple symmetries.
See _exptl_crystals.key.
;
_name.category_id space_group
_name.object_id id
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__space_group.IT_number
_definition.id '_space_group.IT_number'
loop_
_alias.definition_id
'_space_group.IT_number'
'_space_group_IT_number'
_definition.update 2012-11-22
_description.text
;
The number as assigned in International Tables for Crystallography
Vol A, specifying the proper affine class (i.e. the orientation
preserving affine class) of space groups (crystallographic space
group type) to which the space group belongs. This number defines
the space group type but not the coordinate system expressed.
;
_name.category_id space_group
_name.object_id IT_number
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Integer
_enumeration.range 1:
save_
save__space_group.name_H_M_alt
_definition.id '_space_group.name_H_M_alt'
loop_
_alias.definition_id
'_space_group.name_H_M_alt'
'_space_group_name_H-M_alt'
'_space_group.name_H-M_alt'
_definition.update 2013-03-09
_description.text
;
_space_group.name_H_M_alt allows for any Hermann-Mauguin symbol
to be given. The way in which this item is used is determined
by the user and in general is not intended to be interpreted by
computer. It may, for example, be used to give one of the
extended Hermann-Mauguin symbols given in Table 4.3.1 of
International Tables for Crystallography Vol. A (1995) or
a Hermann-Mauguin symbol for a conventional or unconventional
setting.
Each component of the space group name is separated by a
space or underscore. The use of space is strongly
recommended. The underscore is only retained because it
was used in earlier archived files. It should not be
used in new CIFs. Subscripts should appear without special
symbols. Bars should be given as negative signs before the
numbers to which they apply.
The commonly used Hermann-Mauguin symbol determines the space
group type uniquely but a given space group type may be
described by more than one Hermann-Mauguin symbol. The space
group type is best described using _space_group_IT_number.
The Hermann-Mauguin symbol may contain information on the
choice of basis though not on the choice of origin. To
define the setting uniquely use _space_group.name_Hall or
list the symmetry operations.
;
_name.category_id space_group
_name.object_id name_H_M_alt
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
_description_example.detail
'P 1 21/m 1' 'space group No. 10'
'P 2/n 2/n 2/n (origin at -1)' 'space group No. 48 origin 2'
'R -3 2/m' 'space group No. 166 rhomb'
; loop_
_space_group.id
_space_group.name_H_M_alt
'1' 'C m c m'
'2' 'C 2/c 2/m 21/m'
'3' 'A m a m'
; 'three examples for space group No. 63'
save_
save__space_group.name_Hall
_definition.id '_space_group.name_Hall'
loop_
_alias.definition_id
'_space_group.name_Hall'
'_space_group_name_Hall'
_definition.update 2012-11-22
_description.text
;
Space group symbol defined by Hall. Each component of the
space group name is separated by a space or an underscore.
The use of space is strongly recommended because it specifies
the coordinate system. The underscore in the name is only
retained because it was used in earlier archived files. It
should not be used in new CIFs.
Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525
[See also International Tables for Crystallography,
Vol.B (1993) 1.4 Appendix B]
;
_name.category_id space_group
_name.object_id name_Hall
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'P 2ac 2n'
'-R 3 2"'
'P 61 2 2 (0 0 -1)'
save_
save_SPACE_GROUP_SYMOP
_definition.id SPACE_GROUP_SYMOP
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to describe symmetry equivalent sites
in the crystal unit cell.
;
_name.category_id SPACE_GROUP
_name.object_id SPACE_GROUP_SYMOP
_category.key_id '_space_group_symop.key'
_category.key_list ['_space_group_symop.id']
save_
save__space_group_symop.id
_definition.id '_space_group_symop.id'
loop_
_alias.definition_id
'_space_group_symop.id'
'_space_group_symop_id'
'_space_group_symop.sg_id'
'_space_group_symop_sg_id'
_definition.update 2012-11-22
_description.text
;
A sequential number that identifies each symmetry operation.
The identity operation (i.e. _space_group_symop.operation_xyz
set to 'x,y,z') should be set to 1.
;
_name.category_id space_group_symop
_name.object_id id
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Index
_enumeration.range 1:
save_
save__space_group_symop.key
_definition.id '_space_group_symop.key'
loop_
_alias.definition_id
'_space_group_symop.key'
_definition.update 2012-11-22
_description.text
;
Value is a unique key to a set of space_group_symop items
in a looped list.
;
_name.category_id space_group_symop
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Index
loop_
_method.purpose
_method.expression
Evaluation ' _symmetry_equiv.key = _space_group_symop.id'
save_
save__space_group_symop.operation_xyz
_definition.id '_space_group_symop.operation_xyz'
loop_
_alias.definition_id
'_space_group_symop.operation_xyz'
'_space_group_symop_operation_xyz'
_definition.update 2012-11-22
_description.text
;
A parsable string giving one of the symmetry operations of the
space group in algebraic form. If W is a matrix representation
of the rotational part of the symmetry operation defined by the
positions and signs of x, y and z, and w is a column of
translations defined by fractions, an equivalent position
X' is generated from a given position X by the equation
X' = WX + w
(Note: X is used to represent bold_italics_x in International
Tables for Crystallography Vol. A, Part 5)
When a list of symmetry operations is given, it must contain
a complete set of coordinate representatives which generates
all the operations of the space group by the addition of
all primitive translations of the space group. Such
representatives are to be found as the coordinates of
the general-equivalent position in International Tables for
Crystallography Vol. A (2002), to which it is necessary to
add any centring translations shown above the
general-equivalent position.
That is to say, it is necessary to list explicitly all the
symmetry operations required to generate all the atoms in
the unit cell defined by the setting used.
;
_name.category_id space_group_symop
_name.object_id operation_xyz
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
_description_example.detail
'x,1/2-y,1/2+z' 'glide reflection through the plane (x,1/4,z) with glide vector (1/2)c'
save_
save_SYMMETRY
_definition.id SYMMETRY
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items used to describe symmetry information
used in crystallographic structure studies.
;
_name.category_id EXPTL
_name.object_id SYMMETRY
save_
save__symmetry.cell_setting
_definition.id '_symmetry.cell_setting'
loop_
_alias.definition_id
'_symmetry.cell_setting'
'_symmetry_cell_setting'
'_space_group_crystal_system'
_definition.update 2013-04-11
_description.text
;
Code for cell settings for this space-group symmetry.
;
_name.category_id symmetry
_name.object_id cell_setting
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
triclinic
monoclinic
orthorhombic
tetragonal
rhombohedral
trigonal
hexagonal
cubic
_enumeration.default triclinic
loop_
_method.purpose
_method.expression
Validation
;
setting = _symmetry.cell_setting
a = _cell_length.a
b = _cell_length.b
c = _cell_length.c
d = 0.01
alp = _cell_angle.alpha
bet = _cell_angle.beta
gam = _cell_angle.gamma
warn_len = 'Possible mismatch between cell lengths and cell setting'
warn_ang = 'Possible mismatch between cell angles and cell setting'
If(setting == 'triclinic') {
If( Abs(a-b)<d || Abs(a-c)<d || Abs(b-c)<d ) Alert('B', warn_len)
If( Abs(alp-90)<d || Abs(bet-90)<d || Abs(gam-90)<d ) Alert('B', warn_ang)
}
Else If(setting == 'monoclinic') {
If(( Abs(a-b)<d && Abs(a-c)<d ) ||
( Abs(a-b)<d && Abs(b-c)<d ) ||
( Abs(a-c)<d && Abs(b-c)<d )) Alert('B', warn_len)
If( Abs(alp-90)<d && Abs(bet-90)<d && Abs(gam-90)<d ) Alert('B', warn_ang)
If(( Abs(alp-90)>d && Abs(bet-90)>d ) ||
( Abs(alp-90)>d && Abs(gam-90)>d ) ||
( Abs(bet-90)>d && Abs(gam-90)>d ) ) Throw( warn_ang)
}
Else If(setting == 'orthorhombic') {
If( Abs(a-b)<d || Abs(a-c)<d || Abs(b-c)<d ) Alert('B',warn_len)
If( Abs(alp-90)>d || Abs(bet-90)>d || Abs(gam-90)>d ) Throw( warn_ang)
}
Else If(setting == 'tetragonal') {
If( Abs(a-b)<d && Abs(a-c)<d && Abs(b-c)<d ) Alert('B',warn_len)
If( Abs(a-b)>d && Abs(a-c)>d ) Throw( warn_len)
If( Abs(alp-90)>d || Abs(bet-90)>d || Abs(gam-90)>d ) Throw( warn_ang)
}
Else If(setting == 'trigonal' || setting == 'hexagonal') {
If( Abs(a-b)<d && Abs(a-c)<d && Abs(b-c)<d ) Alert('B', warn_len)
If( Abs(a-b)>d && Abs(a-c)>d ) Throw( warn_len)
If( Abs(alp-90)<d && Abs(bet-90)<d && Abs(gam-90)<d ) Throw( warn_ang)
If( Abs(gam-120)>d || Abs(alp-90)>d || Abs(bet-90)>d) Throw( warn_ang)
}
Else If(setting == 'rhombohedral') {
If( Abs(a-b)>d || Abs(a-c)>d || Abs(b-c)>d ) Throw( warn_len)
If( Abs(alp-90)<d || Abs(bet-90)<d || Abs(gam-90)<d ) Alert('B', warn_ang)
If( Abs(alp-bet)>d || Abs(alp-gam)>d || Abs(bet-gam)>d) Throw( warn_ang)
}
Else If(setting == 'cubic') {
If( Abs(a-b)>d || Abs(a-c)>d || Abs(b-c)>d ) Throw( warn_len)
If( Abs(alp-90)>d || Abs(bet-90)>d || Abs(gam-90)>d ) Throw( warn_ang)
}
;
save_
save__symmetry.Int_Tables_number
_definition.id '_symmetry.Int_Tables_number'
loop_
_alias.definition_id
'_symmetry.Int_Tables_number'
'_symmetry_Int_Tables_number'
_definition.update 2012-11-22
_description.text
;
Space-group number from International Tables for Cryst., Vol. A.
;
_name.category_id symmetry
_name.object_id Int_Tables_number
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Index
_enumeration.range 1:230
save_
save__symmetry.multiplicity
_definition.id '_symmetry.multiplicity'
loop_
_alias.definition_id
'_symmetry.multiplicity'
_definition.update 2012-11-22
_description.text
;
Number of unique symmetry elements in the space group.
;
_name.category_id symmetry
_name.object_id multiplicity
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Count
_enumeration.range 1:192
loop_
_method.purpose
_method.expression
Evaluation
;
n = 0
Loop s as symmetry_equiv n += 1
_symmetry.multiplicity = n
;
save_
save__symmetry.space_group_name_H_M
_definition.id '_symmetry.space_group_name_H_M'
loop_
_alias.definition_id
'_symmetry.space_group_name_H_M'
'_symmetry_space_group_name_H-M'
'_symmetry.space_group_name_H-M'
_definition.update 2013-04-07
_description.text
;
Hermann-Mauguin space-group symbol. Note that the H-M symbol does
not necessarily contain complete information about the symmetry
and the space-group origin. If used always supply the FULL symbol
from International Tables for Crystallography, Vol. A (1987) and
indicate the origin and the setting if it is not implicit. If
there is any doubt that the equivalent positions can be uniquely
deduced from this symbol specify the _symmetry_equiv.pos_as_xyz
or *_Hall data items as well. Leave spaces between symbols
referring to different axes.
;
_name.category_id symmetry
_name.object_id space_group_name_H_M
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'P 1 21/m 1'
'P 2/n 2/n 2/n (origin at -1)'
'R -3 2/m'
save_
save__symmetry.space_group_name_Hall
_definition.id '_symmetry.space_group_name_Hall'
loop_
_alias.definition_id
'_symmetry.space_group_name_Hall'
'_symmetry_space_group_name_Hall'
_definition.update 2012-11-22
_description.text
;
Space-group symbol as described by Hall. This symbol gives the
space-group setting explicitly. Leave spaces between the separate
components of the symbol.
Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525.
;
_name.category_id symmetry
_name.object_id space_group_name_Hall
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'P 2ac 2n'
'-R 3 2"'
'P 61 2 2 (0 0 -1)'
save_
save_SYMMETRY_EQUIV
_definition.id SYMMETRY_EQUIV
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to describe symmetry equivalent sites
in the crystal unit cell.
;
_name.category_id SYMMETRY
_name.object_id SYMMETRY_EQUIV
_category.key_id '_symmetry_equiv.key'
_category.key_list ['_symmetry_equiv.pos_site_id']
save_
save__symmetry_equiv.key
_definition.id '_symmetry_equiv.key'
loop_
_alias.definition_id
'_symmetry_equiv.key'
_definition.update 2012-11-22
_description.text
;
Value is a unique key to a set of SYMMETRY_EQUIV items
in a looped list.
;
_name.category_id symmetry_equiv
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Index
loop_
_method.purpose
_method.expression
Evaluation ' _symmetry_equiv.key = _symmetry_equiv.pos_site_id'
save_
save__symmetry_equiv.pos_as_xyz
_definition.id '_symmetry_equiv.pos_as_xyz'
loop_
_alias.definition_id
'_symmetry_equiv.pos_as_xyz'
'_symmetry_equiv_pos_as_xyz'
_definition.update 2012-11-22
_description.text
;
Symmetry equivalent position in the 'xyz' representation. Except
for the space group P1, this data will be repeated in a loop.
The format of the data item is as per International Tables for
Crystallography, Vol. A. (1987). All equivalent positions should
be entered, including those for lattice centring and a centre of
symmetry, if present.
;
_name.category_id symmetry_equiv
_name.object_id pos_as_xyz
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'-y+x,-y,1/3+z'
save_
save__symmetry_equiv.pos_site_id
_definition.id '_symmetry_equiv.pos_site_id'
loop_
_alias.definition_id
'_symmetry_equiv.pos_site_id'
'_symmetry_equiv_pos_site_id'
'_symmetry_equiv.id'
_definition.update 2012-12-30
_description.text
;
Index identifying each entry in the _symmetry_equiv.pos_as_xyz
list. It is normally the sequence number of the entry in that
list, and should be identified with the code 'n' in the geometry
symmetry codes of the form 'n_klm'.
;
_name.category_id symmetry_equiv
_name.object_id pos_site_id
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Index
_enumeration.range 1:
loop_
_method.purpose
_method.expression
Evaluation
;
_symmetry_equiv.pos_site_id = Current_Row(symmetry_equiv) + 1
;
save_
save__symmetry_equiv.R
_definition.id '_symmetry_equiv.R'
loop_
_alias.definition_id
'_symmetry_equiv.R'
_definition.update 2012-11-22
_description.text
;
A matrix containing the symmetry rotation operations of a space group
| r11 r12 r13 |
R = | r21 r22 r23 |
| r31 r32 r33 |
;
_name.category_id symmetry_equiv
_name.object_id R
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3 3]
loop_
_method.purpose
_method.expression
Evaluation
;
sm = _symmetry_equiv.Seitz_matrix
_symmetry_equiv.R = [[sm[0,0],sm[0,1],sm[0,2]],
[sm[1,0],sm[1,1],sm[1,2]],
[sm[2,0],sm[2,1],sm[2,2]]]
;
save_
save__symmetry_equiv.RT
_definition.id '_symmetry_equiv.RT'
loop_
_alias.definition_id
'_symmetry_equiv.RT'
_definition.update 2012-11-22
_description.text
;
The TRANSPOSE of the symmetry rotation matrix representing the point
group opertions of the space group
| r11 r21 r31 |
RT = | r12 r22 r32 |
| r13 r23 r33 |
;
_name.category_id symmetry_equiv
_name.object_id RT
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3 3]
loop_
_method.purpose
_method.expression
Evaluation
;
_symmetry_equiv.RT = Transpose (_symmetry_equiv.R)
;
save_
save__symmetry_equiv.Seitz_matrix
_definition.id '_symmetry_equiv.Seitz_matrix'
loop_
_alias.definition_id
'_symmetry_equiv.Seitz_matrix'
_definition.update 2012-11-22
_description.text
;
A matrix containing the symmetry operations of a space group
in 4x4 Seitz format.
| r11 r12 r13 t1 |
| R T | | r21 r22 r23 t2 |
| 0 1 | | r31 r32 r33 t3 |
| 0 0 0 1 |
;
_name.category_id symmetry_equiv
_name.object_id Seitz_matrix
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [4 4]
loop_
_method.purpose
_method.expression
Evaluation
;
_symmetry_equiv.Seitz_matrix = SeitzFromJones (_symmetry_equiv.pos_as_xyz)
;
save_
save__symmetry_equiv.T
_definition.id '_symmetry_equiv.T'
loop_
_alias.definition_id
'_symmetry_equiv.T'
_definition.update 2012-11-22
_description.text
;
A vector containing the symmetry translation operations of a space group.
;
_name.category_id symmetry_equiv
_name.object_id T
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
sm = _symmetry_equiv.Seitz_matrix
_symmetry_equiv.T = [sm[0,3],sm[1,3],sm[2,3]]
;
save_
save_FUNCTION
_definition.id FUNCTION
_definition.scope Category
_definition.class Functions
_definition.update 2012-12-18
_description.text
;
The crystallographic functions the invoked in the definition
methods of CORE STRUCTURE data items defined and used with in
the Crystallographic Information Framework (CIF).
;
_name.category_id CIF_CORE
_name.object_id FUNCTION
save_
save__function.AtomType
_definition.id '_function.AtomType'
_definition.update 2013-04-17
_description.text
;
The function
r = AtomType( s )
returns an atom type symbol (element name) from the atom site label.
;
_name.category_id function
_name.object_id AtomType
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation
;
Function AtomType( s :[Single, Code]) { # atom label
m = Len(s)
n = 1
If (m > 1 and s[1] not in '0123456789') n = 2
If (m > 2 and s[2] in '+-' ) n = 3
If (m > 3 and s[3] in '+-' ) n = 4
AtomType = s[0:n]
}
;
save_
save__function.Closest
_definition.id '_function.Closest'
_definition.update 2012-10-16
_description.text
;
The function
u, d = Closest( v, u )
returns the real coordinate vector U which is the closest cell-
translated occurence of the vector V to the vector W. D is the
cell translation vector required to move V to U.
;
_name.category_id function
_name.object_id Closest
_type.purpose Number
_type.source Derived
_type.container List
_type.contents 'Matrix(Real,Real,Real)'
_type.dimension [2]
loop_
_method.purpose
_method.expression
Evaluation
;
Function Closest( v :[Matrix, Real], # coord vector to be cell translated
w :[Matrix, Real]) { # target vector
d = v - w
t = Int( Mod( 99.5 + d, 1.0 ) - d )
Closest = List ( v+t, t )
}
;
save_
save__function.SeitzFromJones
_definition.id '_function.SeitzFromJones'
_definition.update 2013-04-24
_description.text
;
The function
s = SeitzFromJones( j )
returns a 4x4 Seitz matrix from the Jones faithful representation of
the equivalent position which is a character string e.g. 1/2+x,-x,z.
;
_name.category_id function
_name.object_id SeitzFromJones
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [4 4]
loop_
_method.purpose
_method.expression
Evaluation
;
Function SeitzFromJones( j :[Single, Text]) { # Jones symmetry notation
joneschrs = "123456xyz/,+- "
s = Matrix([[0,0,0,0],[0,0,0,0],[0,0,0,0],[0,0,0,1]])
axis = 0
sign = 1
inum = 0
do i=0,Len(j)-1 {
c = j[i]
If (c not in joneschrs) print 'illegal char in symmetry xyz'
If (c == ' ') Next
If (c == ',') {
axis += 1
inum = 0
sign = 1
}
Else If (c == '+') sign = +1
Else If (c == '-') sign = -1
Else If (c == 'x') s[axis,0] = sign
Else If (c == 'y') s[axis,1] = sign
Else If (c == 'z') s[axis,2] = sign
Else {
If (inum == 0) m = AtoI(c)
If (inum == 1 and c != '/') print 'illegal num in symmetry xyz'
If (inum == 2) {
n = AtoI(c)
If(n == 5) print 'illegal translation in symmetry xyz'
s[axis,3] = Mod(10.+ Float(sign*m)/Float(n), 1.)
sign = 1
}
inum += 1
} }
SeitzFromJones = s
}
;
save_
save__function.SymEquiv
_definition.id '_function.SymEquiv'
_definition.update 2014-04-17
_description.text
;
The function
xyz' = SymEquiv( symop, xyz )
returns a fractional coordinate vector xyz' which is input vector
xyz transformed by the input symop 'n_pqr' applied to the symmetry
equivalent matrix extracted from the category symmetry_equiv.
;
_name.category_id function
_name.object_id SymEquiv
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
Function SymEquiv( c :[Single, Symop], # symop string n_pqr
x :[Matrix, Real] ){ # fract coordinate vector
s = symmetry_equiv [ SymKey( c ) ]
SymEquiv = s.R * x + s.T + SymLat( c )
}
;
save_
save__function.SymKey
_definition.id '_function.SymKey'
_definition.update 2012-12-17
_description.text
;
The function
m = SymKey( s )
returns an integer index to the Seitz matrices from the character
string of the form 'n_pqr'.
;
_name.category_id function
_name.object_id SymKey
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Index
_enumeration.range 1:192
loop_
_method.purpose
_method.expression
Evaluation
;
Function SymKey( s :[Single, Symop]) { # symop string
If (s == '.') n = 1
Else n = AtoI(s[0])
SymKey = n # index from 1
}
;
save_
save__function.SymLat
_definition.id '_function.SymLat'
_definition.update 2013-03-10
_description.text
;
The function
v = SymLat( s )
returns a vector of the cell translations applied to the coordinates
from the character string of the form 'n_pqr'. i.e. p-5, q-5, r-5.
;
_name.category_id function
_name.object_id SymLat
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.contents Integer
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
Function SymLat( s :[Single, Symop]) { # symop string
If (s[0] == ' ') v = [ 5, 5, 5 ]
Else v = [ AtoI(s[2]), AtoI(s[3]), AtoI(s[4]) ]
SymLat = v - 5
}
;
save_
save__function.Symop
_definition.id '_function.Symop'
_definition.update 2006-06-30
_description.text
;
The function
s = Symop( n, t )
returns a character string of the form 'n_pqr' where n is the
symmetry equivalent site number and [p,q,r] is the cell translation
vector PLUS [5,5,5].
;
_name.category_id function
_name.object_id Symop
_type.purpose Composite
_type.source Derived
_type.container Single
_type.contents Symop
loop_
_method.purpose
_method.expression
Evaluation
;
Function Symop( n :[Single, Integer], # symmetry equivalent site number
t :[List , Integer]) { # cell translation vector
d = t + 5
Symop = `n` + '_' + `d[0]` + `d[1]` + `d[2]`
}
;
save_
save_MODEL
_definition.id MODEL
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
Items in the MODEL Category specify data for the crystal structure
postulated and modelled from the atomic coordinates derived and
refined from the diffraction information. The structural model is
described principally in terms of the geometry of the 'connected'
atom sites and the crystal symmetry in which they reside.
;
_name.category_id CIF_CORE
_name.object_id MODEL
save_
save_GEOM
_definition.id GEOM
_definition.scope Category
_definition.class Set
_definition.update 2012-11-22
_description.text
;
The CATEGORY of data items used to specify the geometry
of the structural model as derived from the atomic sites.
The geometry is expressed in terms of the interatomic
angles (GEOM_ANGLE data), covalent bond distances
(GEOM_BOND data), contact distances (GEOM_CONTACT data),
hydrogen bonds (GEOM_HBOND data) and torsion geometry
(GEOM_TORSION data).
Geometry data are usually redundant, in that they can be
calculated from other more fundamental quantities in the data
block. However, they serve the dual purposes of providing a
check on the correctness of both sets of data and of enabling
the most important geometric data to be identified for
publication by setting the appropriate publication flag.
;
_name.category_id MODEL
_name.object_id GEOM
save_
save__geom.bond_distance_incr
_definition.id '_geom.bond_distance_incr'
loop_
_alias.definition_id
'_geom.bond_distance_incr'
_definition.update 2012-11-22
_description.text
;
Increment added to the bond radii for the atomic species to
specify the maximum permitted "bonded" distance between two
atom sites.
;
_name.category_id geom
_name.object_id bond_distance_incr
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.default 0.2
_units.code angstroms
save_
save__geom.bond_distance_min
_definition.id '_geom.bond_distance_min'
loop_
_alias.definition_id
'_geom.bond_distance_min'
_definition.update 2012-11-22
_description.text
;
Minimum permitted "bonded" distance between two atom sites.
;
_name.category_id geom
_name.object_id bond_distance_min
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.default 0.2
_units.code angstroms
save_
save__geom.contact_distance_incr
_definition.id '_geom.contact_distance_incr'
loop_
_alias.definition_id
'_geom.contact_distance_incr'
_definition.update 2012-11-22
_description.text
;
Increment added to the bond radii for the atomic species to
specify the maximum permitted "contact" distance between two
"non-bonded" atom sites.
;
_name.category_id geom
_name.object_id contact_distance_incr
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.default 0.2
_units.code angstroms
save_
save__geom.contact_distance_min
_definition.id '_geom.contact_distance_min'
loop_
_alias.definition_id
'_geom.contact_distance_min'
_definition.update 2012-11-22
_description.text
;
Minimum permitted "contact" distance between two "non-bonded" atom sites.
;
_name.category_id geom
_name.object_id contact_distance_min
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.default 0.2
_units.code angstroms
save_
save__geom.special_details
_definition.id '_geom.special_details'
loop_
_alias.definition_id
'_geom.special_details'
'_geom_special_details'
'_geom.details'
_definition.update 2012-11-22
_description.text
;
Description of geometry information not covered by the existing data
names in the geometry categories, such as least-squares planes.
;
_name.category_id geom
_name.object_id special_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_GEOM_ANGLE
_definition.id GEOM_ANGLE
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to specify the geometry angles in the
structural model as derived from the atomic sites.
;
_name.category_id GEOM
_name.object_id GEOM_ANGLE
_category.key_id '_geom_angle.key'
_category.key_list ['_geom_angle.atom_site_label_1'
'_geom_angle.atom_site_label_2'
'_geom_angle.atom_site_label_3'
'_geom_angle.site_symmetry_1' '_geom_angle.site_symmetry_2'
'_geom_angle.site_symmetry_3']
loop_
_method.purpose
_method.expression
Evaluation
;
dmin = _geom.bond_distance_min
Loop m1 as model_site :i { # loop vertex model site
rad1 = m1.radius_bond + _geom.bond_distance_incr
Loop m2 as model_site :j { # loop first target site
If (i==j or m1.mole_index != m2.mole_index) Next
v1 = m2.Cartn_xyz - m1.Cartn_xyz
d1 = Norm (v1)
If (d1<dmin or d1>(rad1+m2.radius_bond)) Next
rad2 = m2.radius_bond + _geom.bond_distance_incr
Loop m3 as model_site :k>j { # loop second target site
If (i==k or m1.mole_index != m3.mole_index) Next
v2 = m3.Cartn_xyz - m1.Cartn_xyz
d2 = Norm (v2)
If (d2<dmin or d2>(rad2+m3.radius_bond)) Next
angle = Acosd ( v1*v2 / (d1*d2) )
geom_angle( .id = List ( m2.id, m1.id, m3.id ),
.distances = List ( d1, d2 ),
.value = angle )
} } }
;
save_
save__geom_angle.atom_site_label_1
_definition.id '_geom_angle.atom_site_label_1'
loop_
_alias.definition_id
'_geom_angle.atom_site_label_1'
'_geom_angle_atom_site_label_1'
'_geom_angle.atom_site_id_1'
_name.category_id geom_angle
_name.object_id atom_site_label_1
_type.contents Code
_type.purpose Encode
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell.
;
_type.source Assigned
_name.linked_item_id '_atom_site.label'
_type.container Single
_definition.update 2014-06-16
save_
save__geom_angle.atom_site_label_2
_definition.id '_geom_angle.atom_site_label_2'
loop_
_alias.definition_id
'_geom_angle.atom_site_label_2'
'_geom_angle_atom_site_label_2'
'_geom_angle.atom_site_id_2'
_name.category_id geom_angle
_name.object_id atom_site_label_2
_type.contents Code
_type.purpose Encode
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell.
;
_type.source Assigned
_name.linked_item_id '_atom_site.label'
_type.container Single
_definition.update 2014-06-16
save_
save__geom_angle.atom_site_label_3
_definition.id '_geom_angle.atom_site_label_3'
loop_
_alias.definition_id
'_geom_angle.atom_site_label_3'
'_geom_angle_atom_site_label_3'
'_geom_angle.atom_site_id_3'
_name.category_id geom_angle
_name.object_id atom_site_label_3
_type.contents Code
_type.purpose Encode
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell.
;
_type.source Assigned
_name.linked_item_id '_atom_site.label'
_type.container Single
_definition.update 2014-06-16
save_
save__geom_angle.distances
_definition.id '_geom_angle.distances'
loop_
_alias.definition_id
'_geom_angle.distances'
_definition.update 2012-11-22
_description.text
;
The pair of distances between sites 1 - 2 and 2 - 3.
;
_name.category_id geom_angle
_name.object_id distances
_type.purpose Measurand
_type.source Derived
_type.container List
_type.contents Real
_type.dimension [2]
_units.code angstroms
save_
save__geom_angle.id
_definition.id '_geom_angle.id'
loop_
_alias.definition_id
'_geom_angle.id'
_definition.update 2012-11-22
_description.text
;
Atom site labels and symmetry operators as pairs for each of the
three atom sites which identify the angle. The second label-symop
pair in the list identifies the site at the apex of the angle.
;
_name.category_id geom_angle
_name.object_id id
_type.purpose Composite
_type.source Derived
_type.container List
_type.contents 'List(Code,Symop)'
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With a as geom_angle
_geom_angle.id = [[ a.atom_site_label_1, a.site_symmetry_1 ],
[ a.atom_site_label_2, a.site_symmetry_2 ],
[ a.atom_site_label_3, a.site_symmetry_3 ]]
;
save_
save__geom_angle.key
_definition.id '_geom_angle.key'
loop_
_alias.definition_id
'_geom_angle.key'
_definition.update 2012-11-22
_description.text
;
Value is a unique key to a set of GEOM_ANGLE items
in a looped list.
;
_name.category_id geom_angle
_name.object_id key
_type.purpose Key
_type.source Related
_type.container List
_type.contents 'List(Code,Symop)'
_type.dimension [3]
loop_
_method.purpose
_method.expression
Definition ' _type.contents = Type_Contents(geom_angle.id)'
Evaluation ' _geom_angle.key = _geom_angle.id'
save_
save__geom_angle.publ_flag
_definition.id '_geom_angle.publ_flag'
loop_
_alias.definition_id
'_geom_angle.publ_flag'
'_geom_angle_publ_flag'
_definition.update 2012-11-22
_description.text
;
Code signals if the angle is referred to in a publication or
should be placed in a table of significant angles.
;
_name.category_id geom_angle
_name.object_id publ_flag
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
no 'do not include angle in special list'
n 'abbreviation for "no"'
yes 'do include angle in special list'
y 'abbreviation for "yes"'
_enumeration.default no
save_
save__geom_angle.site_symmetry_1
_definition.id '_geom_angle.site_symmetry_1'
loop_
_alias.definition_id
'_geom_angle.site_symmetry_1'
'_geom_angle_site_symmetry_1'
_name.category_id geom_angle
_name.object_id site_symmetry_1
_type.contents Symop
_type.purpose Composite
_description.text
;
The set of data items which specify the symmetry operation codes
which must be applied to the atom sites involved in the geometry angle.
The symmetry code of each atom site as the symmetry-equivalent position
number 'n' and the cell translation number 'klm'. These numbers are
combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site.fract_xyz. It must match a
number given in _symmetry_equiv.pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
;
_enumeration.default 1_555
_type.source Derived
_type.container Single
_definition.update 2014-06-29
loop_
_description_example.case
_description_example.detail
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
. 'no symmetry or translation to site'
save_
save__geom_angle.site_symmetry_2
_definition.id '_geom_angle.site_symmetry_2'
loop_
_alias.definition_id
'_geom_angle.site_symmetry_2'
'_geom_angle_site_symmetry_2'
_name.category_id geom_angle
_name.object_id site_symmetry_2
_type.contents Symop
_type.purpose Composite
_description.text
;
The set of data items which specify the symmetry operation codes
which must be applied to the atom sites involved in the geometry angle.
The symmetry code of each atom site as the symmetry-equivalent position
number 'n' and the cell translation number 'klm'. These numbers are
combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site.fract_xyz. It must match a
number given in _symmetry_equiv.pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
;
_enumeration.default 1_555
_type.source Derived
_type.container Single
_definition.update 2014-06-29
loop_
_description_example.case
_description_example.detail
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
. 'no symmetry or translation to site'
save_
save__geom_angle.site_symmetry_3
_definition.id '_geom_angle.site_symmetry_3'
loop_
_alias.definition_id
'_geom_angle.site_symmetry_3'
'_geom_angle_site_symmetry_3'
_name.category_id geom_angle
_name.object_id site_symmetry_3
_type.contents Symop
_type.purpose Composite
_description.text
;
The set of data items which specify the symmetry operation codes
which must be applied to the atom sites involved in the geometry angle.
The symmetry code of each atom site as the symmetry-equivalent position
number 'n' and the cell translation number 'klm'. These numbers are
combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site.fract_xyz. It must match a
number given in _symmetry_equiv.pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
;
_enumeration.default 1_555
_type.source Derived
_type.container Single
_definition.update 2014-06-29
loop_
_description_example.case
_description_example.detail
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
. 'no symmetry or translation to site'
save_
save__geom_angle.value
_definition.id '_geom_angle.value'
loop_
_alias.definition_id
'_geom_angle.value'
'_geom_angle'
_definition.update 2012-12-14
_description.text
;
Angle defined by the sites identified by _geom_angle.id
;
_name.category_id geom_angle
_name.object_id value
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range -180.:180.
_units.code degrees
loop_
_method.purpose
_method.expression
Evaluation
;
With a as geom_angle
xc = List()
For [label,symop] in a.id {
xf = SymEquiv(symop, _atom_site[label].fract_xyz)
xc ++= _atom_sites_Cartn_transform.matrix * xf
}
v1,v2 = xc[0]-xc[1], xc[2]-xc[1]
_geom_angle.value = Acosd ( v1 * v2 / ( Norm (v1) * Norm (v2) ) )
;
save_
save__geom_angle.value_su
_definition.id '_geom_angle.value_su'
loop_
_alias.definition_id
'_geom_angle.value_su'
'_geom_angle_su'
'_geom_angle.value_esd'
_definition.update 2012-12-14
_description.text
;
Standard Uncertainty of the
angle defined by the sites identified by _geom_angle.id
;
_name.category_id geom_angle
_name.object_id value_su
_name.linked_item_id '_geom_angle.value'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_units.code degrees
save_
save_GEOM_BOND
_definition.id GEOM_BOND
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to specify the geometry bonds in the
structural model as derived from the atomic sites.
;
_name.category_id GEOM
_name.object_id GEOM_BOND
_category.key_id '_geom_bond.key'
_category.key_list ['_geom_bond.atom_site_label_1'
'_geom_bond.atom_site_label_2' '_geom_bond.site_symmetry_1'
'_geom_bond.site_symmetry_2']
loop_
_method.purpose
_method.expression
Evaluation
;
dmin = _geom.bond_distance_min
Loop m1 as model_site :i {
rad = m1.radius_bond + _geom.bond_distance_incr
Loop m2 as model_site :j {
If (i==j or m1.mole_index != m2.mole_index) Next
d = Norm (m1.Cartn_xyz - m2.Cartn_xyz)
If (d<dmin or d>(rad+m2.radius_bond)) Next
geom_bond( .id = List ( m1.id, m2.id ),
.distance = d )
} }
;
save_
save__geom_bond.atom_site_label_1
_definition.id '_geom_bond.atom_site_label_1'
loop_
_alias.definition_id
'_geom_bond.atom_site_label_1'
'_geom_bond_atom_site_label_1'
'_geom_bond.atom_site_id_1'
_name.category_id geom_bond
_name.object_id atom_site_label_1
_type.contents Code
_type.purpose Encode
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell.
;
_type.source Assigned
_name.linked_item_id '_atom_site.label'
_type.container Single
_definition.update 2014-06-16
save_
save__geom_bond.atom_site_label_2
_definition.id '_geom_bond.atom_site_label_2'
loop_
_alias.definition_id
'_geom_bond.atom_site_label_2'
'_geom_bond_atom_site_label_2'
'_geom_bond.atom_site_id_2'
_name.category_id geom_bond
_name.object_id atom_site_label_2
_type.contents Code
_type.purpose Encode
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell.
;
_type.source Assigned
_name.linked_item_id '_atom_site.label'
_type.container Single
_definition.update 2014-06-16
save_
save__geom_bond.distance
_definition.id '_geom_bond.distance'
loop_
_alias.definition_id
'_geom_bond.distance'
'_geom_bond_distance'
'_geom_bond.dist'
_definition.update 2012-12-14
_description.text
;
Intramolecular bond distance between the sites identified
by _geom_bond.id
;
_name.category_id geom_bond
_name.object_id distance
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code angstroms
loop_
_method.purpose
_method.expression
Evaluation
;
With b as geom_bond
xc = List()
For [label,symop] in b.id {
xf = SymEquiv(symop, _atom_site[label].fract_xyz)
xc ++= _atom_sites_Cartn_transform.matrix * xf
}
_geom_bond.distance = Norm ( xc[0] - xc[1] )
;
save_
save__geom_bond.distance_su
_definition.id '_geom_bond.distance_su'
loop_
_alias.definition_id
'_geom_bond.distance_su'
'_geom_bond_distance_su'
'_geom_bond.dist_esd'
_definition.update 2012-12-14
_description.text
;
Standard Uncertainty of the intramolecular bond distance
between the sites identified by _geom_bond.id
;
_name.category_id geom_bond
_name.object_id distance_su
_name.linked_item_id '_geom_bond.distance'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code angstroms
save_
save__geom_bond.id
_definition.id '_geom_bond.id'
loop_
_alias.definition_id
'_geom_bond.id'
_definition.update 2012-11-22
_description.text
;
Identity of bond distance in terms of the atom site labels and
symmetry operators as pairs for each of the two "bonded" atom sites.
;
_name.category_id geom_bond
_name.object_id id
_type.purpose Composite
_type.source Derived
_type.container List
_type.contents 'List(Code,Symop)'
_type.dimension [2]
loop_
_method.purpose
_method.expression
Evaluation
;
With a as geom_bond
_geom_bond.id = [[ a.atom_site_label_1, a.site_symmetry_1 ],
[ a.atom_site_label_2, a.site_symmetry_2 ]]
;
save_
save__geom_bond.key
_definition.id '_geom_bond.key'
loop_
_alias.definition_id
'_geom_bond.key'
_definition.update 2012-11-22
_description.text
;
Value is a unique key to a set of GEOM_BOND items
in a looped list.
;
_name.category_id geom_bond
_name.object_id key
_type.purpose Key
_type.source Related
_type.container List
_type.contents 'List(Code,Symop)'
_type.dimension [2]
loop_
_method.purpose
_method.expression
Definition ' _type.contents = Type_Contents(geom_bond.id)'
Evaluation ' _geom_bond.key = _geom_bond.id'
save_
save__geom_bond.multiplicity
_definition.id '_geom_bond.multiplicity'
loop_
_alias.definition_id
'_geom_bond.multiplicity'
'_geom_bond_multiplicity'
_definition.update 2013-01-22
_description.text
;
The number of times the given bond appears in the environment
of the atoms labelled _geom_bond.atom_site_label_1. In cases
where the full list of bonds is given, one of the series of
equivalent bonds may be assigned the appropriate multiplicity
while the others are assigned a value of 0.
;
_name.category_id geom_bond
_name.object_id multiplicity
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Count
_enumeration.range 1:
save_
save__geom_bond.publ_flag
_definition.id '_geom_bond.publ_flag'
loop_
_alias.definition_id
'_geom_bond.publ_flag'
'_geom_bond_publ_flag'
_definition.update 2012-11-22
_description.text
;
This code signals whether the angle is referred to in a
publication or should be placed in a table of significant angles.
;
_name.category_id geom_bond
_name.object_id publ_flag
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
no 'do not include bond in special list'
n 'abbreviation for "no"'
yes 'do include bond in special list'
y 'abbreviation for "yes"'
_enumeration.default no
save_
save__geom_bond.site_symmetry_1
_definition.id '_geom_bond.site_symmetry_1'
loop_
_alias.definition_id
'_geom_bond.site_symmetry_1'
'_geom_bond_site_symmetry_1'
_name.category_id geom_bond
_name.object_id site_symmetry_1
_type.contents Symop
_type.purpose Composite
_description.text
;
The set of data items which specify the symmetry operation codes
which must be applied to the atom sites involved in the geometry angle.
The symmetry code of each atom site as the symmetry-equivalent position
number 'n' and the cell translation number 'klm'. These numbers are
combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site.fract_xyz. It must match a
number given in _symmetry_equiv.pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
;
_enumeration.default 1_555
_type.source Derived
_type.container Single
_definition.update 2014-06-29
loop_
_description_example.case
_description_example.detail
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
. 'no symmetry or translation to site'
save_
save__geom_bond.site_symmetry_2
_definition.id '_geom_bond.site_symmetry_2'
loop_
_alias.definition_id
'_geom_bond.site_symmetry_2'
'_geom_bond_site_symmetry_2'
_name.category_id geom_bond
_name.object_id site_symmetry_2
_type.contents Symop
_type.purpose Composite
_description.text
;
The set of data items which specify the symmetry operation codes
which must be applied to the atom sites involved in the geometry angle.
The symmetry code of each atom site as the symmetry-equivalent position
number 'n' and the cell translation number 'klm'. These numbers are
combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site.fract_xyz. It must match a
number given in _symmetry_equiv.pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
;
_enumeration.default 1_555
_type.source Derived
_type.container Single
_definition.update 2014-06-29
loop_
_description_example.case
_description_example.detail
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
. 'no symmetry or translation to site'
save_
save__geom_bond.valence
_definition.id '_geom_bond.valence'
loop_
_alias.definition_id
'_geom_bond.valence'
'_geom_bond_valence'
_definition.update 2012-12-11
_description.text
;
Bond valence calculated from the bond distance.
;
_name.category_id geom_bond
_name.object_id valence
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code electrons
save_
save_GEOM_CONTACT
_definition.id GEOM_CONTACT
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to specify the interatomic
contact distances in the structural model.
;
_name.category_id GEOM
_name.object_id GEOM_CONTACT
_category.key_id '_geom_contact.key'
_category.key_list ['_geom_contact.atom_site_label_1'
'_geom_contact.atom_site_label_2'
'_geom_contact.site_symmetry_1'
'_geom_contact.site_symmetry_2']
loop_
_method.purpose
_method.expression
Evaluation
;
Loop m1 as model_site {
rb = m1.radius_bond + _geom.bond_distance_incr
rc = m1.radius_contact + _geom.contact_distance_incr
Loop m2 as model_site {
If (m2.id[1] != '1_555') Next
radb = rb + m2.radius_bond
radc = rc + m2.radius_contact
label = m2.id[0]
Loop s as symmetry_equiv :ns {
axyz = s.R * m2.fract_xyz + s.T
Do i = -2,2 { Do j = -2,2 { Do k = -2,2 { # cell translations
tran = List ([i,j,k])
bxyz = axyz + tran
cxyz = _atom_sites_Cartn_transform.matrix * bxyz
d = Norm (cxyz - m1.Cartn_xyz)
If (d < radb or d > radc) Next
id = List( m1.id, List( label, Symop(ns+1,tran) ) )
geom_contact( .id = id,
.distance = d )
} } } } } }
;
save_
save__geom_contact.atom_site_label_1
_definition.id '_geom_contact.atom_site_label_1'
loop_
_alias.definition_id
'_geom_contact.atom_site_label_1'
'_geom_contact_atom_site_label_1'
'_geom_contact.atom_site_id_1'
_name.category_id geom_contact
_name.object_id atom_site_label_1
_type.contents Code
_type.purpose Encode
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell.
;
_type.source Assigned
_name.linked_item_id '_atom_site.label'
_type.container Single
_definition.update 2014-06-16
save_
save__geom_contact.atom_site_label_2
_definition.id '_geom_contact.atom_site_label_2'
loop_
_alias.definition_id
'_geom_contact.atom_site_label_2'
'_geom_contact_atom_site_label_2'
'_geom_contact.atom_site_id_2'
_name.category_id geom_contact
_name.object_id atom_site_label_2
_type.contents Code
_type.purpose Encode
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell.
;
_type.source Assigned
_name.linked_item_id '_atom_site.label'
_type.container Single
_definition.update 2014-06-16
save_
save__geom_contact.distance
_definition.id '_geom_contact.distance'
loop_
_alias.definition_id
'_geom_contact.distance'
'_geom_contact_distance'
'_geom_contact.dist'
_definition.update 2012-12-14
_description.text
;
Intermolecular distance between the atomic sites identifyed
by _geom_contact.id
;
_name.category_id geom_contact
_name.object_id distance
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code angstroms
loop_
_method.purpose
_method.expression
Evaluation
;
With c as geom_contact
xc = List()
For [label,symop] in c.id {
xf = SymEquiv(symop, _atom_site[label].fract_xyz)
xc ++= _atom_sites_Cartn_transform.matrix * xf
}
_geom_contact.distance = Norm ( xc[0] - xc[1] )
;
save_
save__geom_contact.distance_su
_definition.id '_geom_contact.distance_su'
loop_
_alias.definition_id
'_geom_contact.distance_su'
'_geom_contact_distance_su'
'_geom_contact.dist_esd'
_definition.update 2012-12-14
_description.text
;
Standard Uncertainty of the intermolecular distance between
the atomic sites identified by _geom_contact.id
;
_name.category_id geom_contact
_name.object_id distance_su
_name.linked_item_id '_geom_contact.distance'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code angstroms
save_
save__geom_contact.id
_definition.id '_geom_contact.id'
loop_
_alias.definition_id
'_geom_contact.id'
_definition.update 2012-11-22
_description.text
;
Atom site labels and symmetry operators as pairs for each of the
two atom sites which define the geom_contact bond.
;
_name.category_id geom_contact
_name.object_id id
_type.purpose Composite
_type.source Derived
_type.container List
_type.contents 'List(Code,Symop)'
_type.dimension [2]
loop_
_method.purpose
_method.expression
Evaluation
;
With a as geom_contact
_geom_contact.id = [[ a.atom_site_label_1, a.site_symmetry_1 ],
[ a.atom_site_label_2, a.site_symmetry_2 ]]
;
save_
save__geom_contact.key
_definition.id '_geom_contact.key'
loop_
_alias.definition_id
'_geom_contact.key'
_definition.update 2012-11-22
_description.text
;
Value is a unique key to a set of GEOM_CONTACT items
in a looped list.
;
_name.category_id geom_contact
_name.object_id key
_type.purpose Key
_type.source Related
_type.container List
_type.contents 'List(Code,Symop)'
_type.dimension [2]
loop_
_method.purpose
_method.expression
Evaluation ' _geom_contact.key = _geom_contact.id'
save_
save__geom_contact.publ_flag
_definition.id '_geom_contact.publ_flag'
loop_
_alias.definition_id
'_geom_contact.publ_flag'
'_geom_contact_publ_flag'
_definition.update 2012-11-22
_description.text
;
This code signals whether the contact distance is referred to
in a publication or should be placed in a list of significant
contact distances.
;
_name.category_id geom_contact
_name.object_id publ_flag
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
no 'do not include distance in special list'
n 'abbreviation for "no"'
yes 'do include distance in special list'
y 'abbreviation for "yes"'
_enumeration.default no
save_
save__geom_contact.site_symmetry_1
_definition.id '_geom_contact.site_symmetry_1'
loop_
_alias.definition_id
'_geom_contact.site_symmetry_1'
'_geom_contact_site_symmetry_1'
_name.category_id geom_contact
_name.object_id site_symmetry_1
_type.contents Symop
_type.purpose Composite
_description.text
;
The set of data items which specify the symmetry operation codes
which must be applied to the atom sites involved in the geometry angle.
The symmetry code of each atom site as the symmetry-equivalent position
number 'n' and the cell translation number 'klm'. These numbers are
combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site.fract_xyz. It must match a
number given in _symmetry_equiv.pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
;
_enumeration.default 1_555
_type.source Derived
_type.container Single
_definition.update 2014-06-29
loop_
_description_example.case
_description_example.detail
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
. 'no symmetry or translation to site'
save_
save__geom_contact.site_symmetry_2
_definition.id '_geom_contact.site_symmetry_2'
loop_
_alias.definition_id
'_geom_contact.site_symmetry_2'
'_geom_contact_site_symmetry_2'
_name.category_id geom_contact
_name.object_id site_symmetry_2
_type.contents Symop
_type.purpose Composite
_description.text
;
The set of data items which specify the symmetry operation codes
which must be applied to the atom sites involved in the geometry angle.
The symmetry code of each atom site as the symmetry-equivalent position
number 'n' and the cell translation number 'klm'. These numbers are
combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site.fract_xyz. It must match a
number given in _symmetry_equiv.pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
;
_enumeration.default 1_555
_type.source Derived
_type.container Single
_definition.update 2014-06-29
loop_
_description_example.case
_description_example.detail
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
. 'no symmetry or translation to site'
save_
save_GEOM_HBOND
_definition.id GEOM_HBOND
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to specify the hydrogen bond
distances in the structural model as derived from atomic sites.
;
_name.category_id GEOM
_name.object_id GEOM_HBOND
_category.key_id '_geom_hbond.key'
_category.key_list ['_geom_hbond.atom_site_label_D'
'_geom_hbond.atom_site_label_H'
'_geom_hbond.atom_site_label_A'
'_geom_hbond.site_symmetry_D' '_geom_hbond.site_symmetry_H'
'_geom_hbond.site_symmetry_A']
save_
save__geom_hbond.angle_DHA
_definition.id '_geom_hbond.angle_DHA'
loop_
_alias.definition_id
'_geom_hbond.angle_DHA'
'_geom_hbond_angle_DHA'
_definition.update 2012-12-14
_description.text
;
Angle subtended by the sites identifyed in _geom_hbond.id.
The hydrogen at site H is at the apex of the angle.
;
_name.category_id geom_hbond
_name.object_id angle_DHA
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range -180.:180.
_units.code degrees
loop_
_method.purpose
_method.expression
Evaluation
;
With h as geom_hbond
xc = List()
For [label,symop] in h.id {
xf = SymEquiv(symop, _atom_site[label].fract_xyz)
xc ++= _atom_sites_Cartn_transform.matrix * xf
}
v1,v2 = xc[0]-xc[1], xc[2]-xc[1]
_geom_hbond.angle_DHA = Acosd ( v1 * v2 / ( Norm (v1) * Norm (v2) ) )
;
save_
save__geom_hbond.angle_DHA_su
_definition.id '_geom_hbond.angle_DHA_su'
loop_
_alias.definition_id
'_geom_hbond.angle_DHA_su'
'_geom_hbond_angle_DHA_su'
'_geom_hbond.angle_DHA_esd'
_definition.update 2012-12-14
_description.text
;
Angle subtended by the sites identifyed in _geom_hbond.id.
The hydrogen at site H is at the apex of the angle.
;
_name.category_id geom_hbond
_name.object_id angle_DHA_su
_name.linked_item_id '_geom_hbond.angle_DHA'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range -180.:180.
_units.code degrees
save_
save__geom_hbond.atom_site_label_A
_definition.id '_geom_hbond.atom_site_label_A'
loop_
_alias.definition_id
'_geom_hbond.atom_site_label_A'
'_geom_hbond_atom_site_label_A'
'_geom_hbond.atom_site_id_A'
_name.category_id geom_hbond
_name.object_id atom_site_label_A
_type.contents Code
_type.purpose Encode
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell.
;
_type.source Assigned
_name.linked_item_id '_atom_site.label'
_type.container Single
_definition.update 2014-06-16
save_
save__geom_hbond.atom_site_label_D
_definition.id '_geom_hbond.atom_site_label_D'
loop_
_alias.definition_id
'_geom_hbond.atom_site_label_D'
'_geom_hbond_atom_site_label_D'
'_geom_hbond.atom_site_id_D'
_name.category_id geom_hbond
_name.object_id atom_site_label_D
_type.contents Code
_type.purpose Encode
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell.
;
_type.source Assigned
_name.linked_item_id '_atom_site.label'
_type.container Single
_definition.update 2014-06-16
save_
save__geom_hbond.atom_site_label_H
_definition.id '_geom_hbond.atom_site_label_H'
loop_
_alias.definition_id
'_geom_hbond.atom_site_label_H'
'_geom_hbond_atom_site_label_H'
'_geom_hbond.atom_site_id_H'
_name.category_id geom_hbond
_name.object_id atom_site_label_H
_type.contents Code
_type.purpose Encode
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell.
;
_type.source Assigned
_name.linked_item_id '_atom_site.label'
_type.container Single
_definition.update 2014-06-16
save_
save__geom_hbond.distance_DA
_definition.id '_geom_hbond.distance_DA'
loop_
_alias.definition_id
'_geom_hbond.distance_DA'
'_geom_hbond_distance_DA'
'_geom_hbond.dist_DA'
_definition.update 2012-12-14
_description.text
;
The set of data items which specify the distance between the
three atom sites identified by _geom_hbond.id.
;
_name.category_id geom_hbond
_name.object_id distance_DA
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
loop_
_method.purpose
_method.expression
Evaluation
;
xc = List()
Do i=0,2,2 {
l,s = _geom_hbond.id [i]
xf = SymEquiv(s, _atom_site[l].fract_xyz)
xc ++= _atom_sites_Cartn_transform.matrix * xf
}
_geom_hbond.distance_DA = Norm ( xc[0] - xc[1] )
;
save_
save__geom_hbond.distance_DA_su
_definition.id '_geom_hbond.distance_DA_su'
loop_
_alias.definition_id
'_geom_hbond.distance_DA_su'
'_geom_hbond_distance_DA_su'
'_geom_hbond.dist_DA_esd'
_definition.update 2012-12-14
_description.text
;
Standard Uncertainty of the
set of data items which specify the distance between the
three atom sites identified by _geom_hbond.id.
;
_name.category_id geom_hbond
_name.object_id distance_DA_su
_name.linked_item_id '_geom_hbond.distance_DA'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__geom_hbond.distance_DH
_definition.id '_geom_hbond.distance_DH'
loop_
_alias.definition_id
'_geom_hbond.distance_DH'
'_geom_hbond_distance_DH'
'_geom_hbond.dist_DH'
_definition.update 2012-12-14
_description.text
;
The set of data items which specify the distance between the
three atom sites identified by _geom_hbond.id.
;
_name.category_id geom_hbond
_name.object_id distance_DH
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
loop_
_method.purpose
_method.expression
Evaluation
;
xc = List()
Do i=0,1 {
l,s = _geom_hbond.id [i]
xf = SymEquiv(s, _atom_site[l].fract_xyz)
xc ++= _atom_sites_Cartn_transform.matrix * xf
}
_geom_hbond.distance_DH = Norm ( xc[0] - xc[1] )
;
save_
save__geom_hbond.distance_DH_su
_definition.id '_geom_hbond.distance_DH_su'
loop_
_alias.definition_id
'_geom_hbond.distance_DH_su'
'_geom_hbond_distance_DH_su'
'_geom_hbond.dist_DH_esd'
_definition.update 2012-12-14
_description.text
;
Standard Uncertainty of the
set of data items which specify the distance between the
three atom sites identified by _geom_hbond.id.
;
_name.category_id geom_hbond
_name.object_id distance_DH_su
_name.linked_item_id '_geom_hbond.distance_DH'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__geom_hbond.distance_HA
_definition.id '_geom_hbond.distance_HA'
loop_
_alias.definition_id
'_geom_hbond.distance_HA'
'_geom_hbond_distance_HA'
'_geom_hbond.dist_HA'
_definition.update 2012-12-14
_description.text
;
The set of data items which specify the distance between the
three atom sites identified by _geom_hbond.id.
;
_name.category_id geom_hbond
_name.object_id distance_HA
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
loop_
_method.purpose
_method.expression
Evaluation
;
xc = List()
Do i=1,2 {
l,s = _geom_hbond.id [i]
xf = SymEquiv(s, _atom_site[l].fract_xyz)
xc ++= _atom_sites_Cartn_transform.matrix * xf
}
_geom_hbond.distance_HA = Norm ( xc[0] - xc[1] )
;
save_
save__geom_hbond.distance_HA_su
_definition.id '_geom_hbond.distance_HA_su'
loop_
_alias.definition_id
'_geom_hbond.distance_HA_su'
'_geom_hbond_distance_HA_su'
'_geom_hbond.dist_HA_esd'
_definition.update 2012-12-14
_description.text
;
Standard Uncertainty of the
set of data items which specify the distance between the
three atom sites identified by _geom_hbond.id.
;
_name.category_id geom_hbond
_name.object_id distance_HA_su
_name.linked_item_id '_geom_hbond.distance_HA'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__geom_hbond.id
_definition.id '_geom_hbond.id'
loop_
_alias.definition_id
'_geom_hbond.id'
_definition.update 2012-11-22
_description.text
;
Atom site labels and symmetry operators as pairs for each of the
three atom sites which define the hydrogen angle and distances.
Site H is at the apex of the angle.
;
_name.category_id geom_hbond
_name.object_id id
_type.purpose Composite
_type.source Derived
_type.container List
_type.contents 'List(Code,Symop)'
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With a as geom_hbond
_geom_hbond.id = [[ a.atom_site_label_D, a.site_symmetry_D ],
[ a.atom_site_label_H, a.site_symmetry_H ],
[ a.atom_site_label_A, a.site_symmetry_A ]]
;
save_
save__geom_hbond.key
_definition.id '_geom_hbond.key'
loop_
_alias.definition_id
'_geom_hbond.key'
_definition.update 2012-11-22
_description.text
;
Value is a unique key to a set of GEOM_HBOND items
in a looped list.
;
_name.category_id geom_hbond
_name.object_id key
_type.purpose Key
_type.source Related
_type.container List
_type.contents 'List(Code,Symop)'
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation ' _geom_hbond.key = _geom_hbond.id'
save_
save__geom_hbond.publ_flag
_definition.id '_geom_hbond.publ_flag'
loop_
_alias.definition_id
'_geom_hbond.publ_flag'
'_geom_hbond_publ_flag'
_definition.update 2012-11-22
_description.text
;
This code signals whether the hydrogen-bond information
is referred to in a publication or should be placed in a
table of significant hydrogen-bond geometry.
;
_name.category_id geom_hbond
_name.object_id publ_flag
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
no 'do not include bond in special list'
n 'abbreviation for "no"'
yes 'do include bond in special list'
y 'abbreviation for "yes"'
_enumeration.default no
save_
save__geom_hbond.site_symmetry_A
_definition.id '_geom_hbond.site_symmetry_A'
loop_
_alias.definition_id
'_geom_hbond.site_symmetry_A'
'_geom_hbond_site_symmetry_A'
_name.category_id geom_hbond
_name.object_id site_symmetry_A
_type.contents Symop
_type.purpose Composite
_description.text
;
The set of data items which specify the symmetry operation codes
which must be applied to the atom sites involved in the geometry angle.
The symmetry code of each atom site as the symmetry-equivalent position
number 'n' and the cell translation number 'klm'. These numbers are
combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site.fract_xyz. It must match a
number given in _symmetry_equiv.pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
;
_enumeration.default 1_555
_type.source Derived
_type.container Single
_definition.update 2014-06-29
loop_
_description_example.case
_description_example.detail
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
. 'no symmetry or translation to site'
save_
save__geom_hbond.site_symmetry_D
_definition.id '_geom_hbond.site_symmetry_D'
loop_
_alias.definition_id
'_geom_hbond.site_symmetry_D'
'_geom_hbond_site_symmetry_D'
_name.category_id geom_hbond
_name.object_id site_symmetry_D
_type.contents Symop
_type.purpose Composite
_description.text
;
The set of data items which specify the symmetry operation codes
which must be applied to the atom sites involved in the geometry angle.
The symmetry code of each atom site as the symmetry-equivalent position
number 'n' and the cell translation number 'klm'. These numbers are
combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site.fract_xyz. It must match a
number given in _symmetry_equiv.pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
;
_enumeration.default 1_555
_type.source Derived
_type.container Single
_definition.update 2014-06-29
loop_
_description_example.case
_description_example.detail
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
. 'no symmetry or translation to site'
save_
save__geom_hbond.site_symmetry_H
_definition.id '_geom_hbond.site_symmetry_H'
loop_
_alias.definition_id
'_geom_hbond.site_symmetry_H'
'_geom_hbond_site_symmetry_H'
_name.category_id geom_hbond
_name.object_id site_symmetry_H
_type.contents Symop
_type.purpose Composite
_description.text
;
The set of data items which specify the symmetry operation codes
which must be applied to the atom sites involved in the geometry angle.
The symmetry code of each atom site as the symmetry-equivalent position
number 'n' and the cell translation number 'klm'. These numbers are
combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site.fract_xyz. It must match a
number given in _symmetry_equiv.pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
;
_enumeration.default 1_555
_type.source Derived
_type.container Single
_definition.update 2014-06-29
loop_
_description_example.case
_description_example.detail
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
. 'no symmetry or translation to site'
save_
save_GEOM_TORSION
_definition.id GEOM_TORSION
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to specify the torsion angles in the
structural model as derived from the atomic sites.
;
_name.category_id GEOM
_name.object_id GEOM_TORSION
_category.key_id '_geom_torsion.key'
_category.key_list ['_geom_torsion.atom_site_label_1'
'_geom_torsion.atom_site_label_2'
'_geom_torsion.atom_site_label_3'
'_geom_torsion.atom_site_label_4'
'_geom_torsion.site_symmetry_1'
'_geom_torsion.site_symmetry_2'
'_geom_torsion.site_symmetry_3'
'_geom_torsion.site_symmetry_4']
loop_
_method.purpose
_method.expression
Evaluation
;
dmin = _geom.bond_distance_min
Loop m1 as model_site :i {
rad1 = m1.radius_bond + _geom.bond_distance_incr
Loop m2 as model_site :j {
If (i==j or m2.mole_index!=m1.mole_index) Next
v21 = m1.Cartn_xyz - m2.Cartn_xyz
d21 = Norm (v21)
If (d21 < dmin or d21 > (rad1+m2.radius_bond)) Next
rad2 = m2.radius_bond + _geom.bond_distance_incr
Loop m3 as model_site :k {
If (k==i or k==j or m3.mole_index!=m2.mole_index) Next
v23 = m3.Cartn_xyz - m2.Cartn_xyz
d23 = Norm (v23)
If (d23 < dmin or d23 > (rad2+m3.radius_bond)) Next
rad3 = m3.radius_bond + _geom.bond_distance_incr
Loop m4 as model_site :l {
If (l==k or l==j or l==i or m4.mole_index!=m3.mole_index) Next
v34 = m4.Cartn_xyz - m3.Cartn_xyz
d34 = Norm (v34)
If (d34 < dmin or d34 > (rad3+m4.radius_bond)) Next
u1 = v21 ^ v23
u2 = v34 ^ v23
angle = Acosd ( u1 * u2 / ( Norm(u1) * Norm(u2) ) )
If ( (u1^u2)*v23 < 0 ) angle = -angle
geom_torsion( .id = List ( m1.id,m2.id,m3.id,m4.id ),
.distances = List ( d21,d23,d34 ),
.angle = angle )
} } } }
;
save_
save__geom_torsion.angle
_definition.id '_geom_torsion.angle'
loop_
_alias.definition_id
'_geom_torsion.angle'
'_geom_torsion'
'_geom_torsion.value'
_definition.update 2012-11-22
_description.text
;
Angle defined by the sites identifyed in _geom_torsion.id.
The torsion-angle definition should be that of Klyne and Prelog.
The vector direction *_label_2 to *_label_3 is the viewing
direction, and the torsion angle is the angle of twist required
to superimpose the projection of the vector between site 2 and
site 1 onto the projection of the vector between site 3 and
site 4. Clockwise torsions are positive, anticlockwise torsions
are negative.
Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523.
;
_name.category_id geom_torsion
_name.object_id angle
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range -180.:180.
_units.code degrees
save_
save__geom_torsion.angle_su
_definition.id '_geom_torsion.angle_su'
loop_
_alias.definition_id
'_geom_torsion.angle_su'
'_geom_torsion_su'
'_geom_torsion.value_esd'
_definition.update 2012-11-22
_description.text
;
Standard Uncertainty of the torsion angle.
;
_name.category_id geom_torsion
_name.object_id angle_su
_name.linked_item_id '_geom_torsion.angle'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_units.code degrees
save_
save__geom_torsion.atom_site_label_1
_definition.id '_geom_torsion.atom_site_label_1'
loop_
_alias.definition_id
'_geom_torsion.atom_site_label_1'
'_geom_torsion_atom_site_label_1'
'_geom_torsion.atom_site_id_1'
_name.category_id geom_torsion
_name.object_id atom_site_label_1
_type.contents Code
_type.purpose Encode
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell.
;
_type.source Assigned
_name.linked_item_id '_atom_site.label'
_type.container Single
_definition.update 2014-06-16
save_
save__geom_torsion.atom_site_label_2
_definition.id '_geom_torsion.atom_site_label_2'
loop_
_alias.definition_id
'_geom_torsion.atom_site_label_2'
'_geom_torsion_atom_site_label_2'
'_geom_torsion.atom_site_id_2'
_name.category_id geom_torsion
_name.object_id atom_site_label_2
_type.contents Code
_type.purpose Encode
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell.
;
_type.source Assigned
_name.linked_item_id '_atom_site.label'
_type.container Single
_definition.update 2014-06-16
save_
save__geom_torsion.atom_site_label_3
_definition.id '_geom_torsion.atom_site_label_3'
loop_
_alias.definition_id
'_geom_torsion.atom_site_label_3'
'_geom_torsion_atom_site_label_3'
'_geom_torsion.atom_site_id_3'
_name.category_id geom_torsion
_name.object_id atom_site_label_3
_type.contents Code
_type.purpose Encode
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell.
;
_type.source Assigned
_name.linked_item_id '_atom_site.label'
_type.container Single
_definition.update 2014-06-16
save_
save__geom_torsion.atom_site_label_4
_definition.id '_geom_torsion.atom_site_label_4'
loop_
_alias.definition_id
'_geom_torsion.atom_site_label_4'
'_geom_torsion_atom_site_label_4'
'_geom_torsion.atom_site_id_4'
_name.category_id geom_torsion
_name.object_id atom_site_label_4
_type.contents Code
_type.purpose Encode
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell.
;
_type.source Assigned
_name.linked_item_id '_atom_site.label'
_type.container Single
_definition.update 2014-06-16
save_
save__geom_torsion.distances
_definition.id '_geom_torsion.distances'
loop_
_alias.definition_id
'_geom_torsion.distances'
_definition.update 2012-11-22
_description.text
;
Distances between sites 1 - 2, 2 - 3 and 3 - 4.
;
_name.category_id geom_torsion
_name.object_id distances
_type.purpose Measurand
_type.source Derived
_type.container List
_type.contents Real
_type.dimension [3]
_units.code angstroms
save_
save__geom_torsion.id
_definition.id '_geom_torsion.id'
loop_
_alias.definition_id
'_geom_torsion.id'
_definition.update 2012-11-22
_description.text
;
Atom site labels and symmetry operators as pairs for each of the
four atom sites which define the torsion angle.
;
_name.category_id geom_torsion
_name.object_id id
_type.purpose Composite
_type.source Derived
_type.container List
_type.contents 'List(Code,Symop)'
_type.dimension [4]
loop_
_method.purpose
_method.expression
Evaluation
;
With a as geom_torsion
_geom_torsion.id = [[ a.atom_site_label_1, a.site_symmetry_1 ],
[ a.atom_site_label_2, a.site_symmetry_2 ],
[ a.atom_site_label_3, a.site_symmetry_3 ],
[ a.atom_site_label_4, a.site_symmetry_4 ]]
;
save_
save__geom_torsion.key
_definition.id '_geom_torsion.key'
loop_
_alias.definition_id
'_geom_torsion.key'
_definition.update 2012-11-22
_description.text
;
Value is a unique key to a set of GEOM_TORSION items
in a looped list.
;
_name.category_id geom_torsion
_name.object_id key
_type.purpose Key
_type.source Related
_type.container List
_type.contents 'List(Code,Symop)'
_type.dimension [4]
loop_
_method.purpose
_method.expression
Definition ' _type.contents = Type_Contents(geom_torsion.id)'
Evaluation ' _geom_torsion.key = _geom_torsion.id'
save_
save__geom_torsion.publ_flag
_definition.id '_geom_torsion.publ_flag'
loop_
_alias.definition_id
'_geom_torsion.publ_flag'
'_geom_torsion_publ_flag'
_definition.update 2012-11-22
_description.text
;
Code signals if the torsion angle is required for publication.
;
_name.category_id geom_torsion
_name.object_id publ_flag
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
Yes Publish
No 'Do not publish'
_enumeration.default No
save_
save__geom_torsion.site_symmetry_1
_definition.id '_geom_torsion.site_symmetry_1'
loop_
_alias.definition_id
'_geom_torsion.site_symmetry_1'
'_geom_torsion_site_symmetry_1'
_name.category_id geom_torsion
_name.object_id site_symmetry_1
_type.contents Symop
_type.purpose Composite
_description.text
;
The set of data items which specify the symmetry operation codes
which must be applied to the atom sites involved in the geometry angle.
The symmetry code of each atom site as the symmetry-equivalent position
number 'n' and the cell translation number 'klm'. These numbers are
combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site.fract_xyz. It must match a
number given in _symmetry_equiv.pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
;
_enumeration.default 1_555
_type.source Derived
_type.container Single
_definition.update 2014-06-29
loop_
_description_example.case
_description_example.detail
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
. 'no symmetry or translation to site'
save_
save__geom_torsion.site_symmetry_2
_definition.id '_geom_torsion.site_symmetry_2'
loop_
_alias.definition_id
'_geom_torsion.site_symmetry_2'
'_geom_torsion_site_symmetry_2'
_name.category_id geom_torsion
_name.object_id site_symmetry_2
_type.contents Symop
_type.purpose Composite
_description.text
;
The set of data items which specify the symmetry operation codes
which must be applied to the atom sites involved in the geometry angle.
The symmetry code of each atom site as the symmetry-equivalent position
number 'n' and the cell translation number 'klm'. These numbers are
combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site.fract_xyz. It must match a
number given in _symmetry_equiv.pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
;
_enumeration.default 1_555
_type.source Derived
_type.container Single
_definition.update 2014-06-29
loop_
_description_example.case
_description_example.detail
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
. 'no symmetry or translation to site'
save_
save__geom_torsion.site_symmetry_3
_definition.id '_geom_torsion.site_symmetry_3'
loop_
_alias.definition_id
'_geom_torsion.site_symmetry_3'
'_geom_torsion_site_symmetry_3'
_name.category_id geom_torsion
_name.object_id site_symmetry_3
_type.contents Symop
_type.purpose Composite
_description.text
;
The set of data items which specify the symmetry operation codes
which must be applied to the atom sites involved in the geometry angle.
The symmetry code of each atom site as the symmetry-equivalent position
number 'n' and the cell translation number 'klm'. These numbers are
combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site.fract_xyz. It must match a
number given in _symmetry_equiv.pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
;
_enumeration.default 1_555
_type.source Derived
_type.container Single
_definition.update 2014-06-29
loop_
_description_example.case
_description_example.detail
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
. 'no symmetry or translation to site'
save_
save__geom_torsion.site_symmetry_4
_definition.id '_geom_torsion.site_symmetry_4'
loop_
_alias.definition_id
'_geom_torsion.site_symmetry_4'
'_geom_torsion_site_symmetry_4'
_name.category_id geom_torsion
_name.object_id site_symmetry_4
_type.contents Symop
_type.purpose Composite
_description.text
;
The set of data items which specify the symmetry operation codes
which must be applied to the atom sites involved in the geometry angle.
The symmetry code of each atom site as the symmetry-equivalent position
number 'n' and the cell translation number 'klm'. These numbers are
combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site.fract_xyz. It must match a
number given in _symmetry_equiv.pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
;
_enumeration.default 1_555
_type.source Derived
_type.container Single
_definition.update 2014-06-29
loop_
_description_example.case
_description_example.detail
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
. 'no symmetry or translation to site'
save_
save_MODEL_SITE
_definition.id MODEL_SITE
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to describe atomic sites and
connections in the proposed atomic model.
;
_name.category_id MODEL
_name.object_id MODEL_SITE
_category.key_id '_model_site.key'
_category.key_list ['_model_site.label' '_model_site.symop']
loop_
_method.purpose
_method.expression
Evaluation
;
atomlist = List()
Loop a as atom_site {
axyz = a.fract_xyz
cxyz = _atom_sites_Cartn_transform.matrix * axyz
radb = _atom_type[a.type_symbol].radius_bond
radc = _atom_type[a.type_symbol].radius_contact
ls = List ( a.label, "1_555" )
atomlist ++= [ls, axyz, cxyz, radb, radc, 0]
}
molelist = List()
dmin = _geom.bond_distance_min
m = 0
n = 0
For [ls1,a1,c1,rb1,rc1,m1] in atomlist {
If (m1 != 0) Next
m += 1
n += 1
molelist ++= [ls1,a1,c1,rb1,rc1,n,m]
atomlist --= [ls1,a1,c1,rb1,rc1,m1]
Repeat {
connect = "no"
For [ls2,a2,c2,rb2,rc2,n2,m2] in molelist {
If (m2 != m) Next
For [ls3,a3,c3,rb3,rc3,m3] in atomlist {
dmax = rb2 + rb3 + _geom.bond_distance_incr
Loop s as symmetry_equiv :ns {
axyz = s.R * a3 + s.T
bxyz,tran = Closest (axyz, a2)
cxyz = _atom_sites_Cartn_transform.matrix *bxyz
d = Norm (cxyz - c2)
If (d > dmin and d < dmax) {
ls = List ( ls3[0], Symop(ns+1, tran) )
If (ls not in Strip(molelist,0)) {
n += 1
molelist ++= [ls,bxyz,cxyz,rb3,rc3,n,m]
atomlist --= [ls3,a3,c3,rb3,rc3,m3]
connect = "yes"
} } } } }
If (connect == "no") Break
} }
For [ls,ax,cx,rb,rc,n,m] in molelist {
model_site( .id = ls,
.fract_xyz = ax,
.Cartn_xyz = cx,
.radius_bond = rb,
.radius_contact = rc,
.index = n,
.mole_index = m )
}
;
save_
save__model_site.adp_eigen_system
_definition.id '_model_site.adp_eigen_system'
loop_
_alias.definition_id
'_model_site.adp_eigen_system'
_definition.update 2012-11-22
_description.text
;
The set of three adp eigenvales and associated eigenvectors
in the form of 4 element List. Each list has the form
(val, vecX, vecY, vecZ)
where the vector elements are direction cosines to the orthogonal
axes X,Y,Z. The lists are sorted in descending magnitude of val.
That is, the list with the largest val is first, and the smallest
val is last.
;
_name.category_id model_site
_name.object_id adp_eigen_system
_type.purpose Measurand
_type.source Derived
_type.container List
_type.contents 'List(Real,Real,Real,Real)'
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
A = _cell.orthogonal_matrix
U = A * _model_site.adp_matrix_beta * Transpose(A) /(2*Pi**2)
_model_site.adp_eigen_system = Eigen( U )
;
save_
save__model_site.adp_matrix_beta
_definition.id '_model_site.adp_matrix_beta'
loop_
_alias.definition_id
'_model_site.adp_matrix_beta'
_definition.update 2013-03-08
_description.text
;
Matrix of dimensionless anisotropic atomic displacement parameters.
;
_name.category_id model_site
_name.object_id adp_matrix_beta
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3 3]
loop_
_method.purpose
_method.expression
Evaluation
;
[label,symop] = _model_site.id
a = atom_site[label]
s = symmetry_equiv[SymKey(symop)]
_model_site.adp_matrix_beta = s.R * a.tensor_beta * s.RT
;
save_
save__model_site.Cartn_xyz
_definition.id '_model_site.Cartn_xyz'
loop_
_alias.definition_id
'_model_site.Cartn_xyz'
_definition.update 2012-11-22
_description.text
;
Vector of Cartesian (orthogonal angstrom) atom site coordinates.
;
_name.category_id model_site
_name.object_id Cartn_xyz
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With m as model_site
_model_site.Cartn_xyz = _atom_sites_Cartn_transform.matrix * m.fract_xyz
;
save_
save__model_site.display_colour
_definition.id '_model_site.display_colour'
loop_
_alias.definition_id
'_model_site.display_colour'
_definition.update 2013-01-23
_description.text
;
Display colour code assigned to this atom site. Note that the
possible colours are enumerated in the colour_RBG list, and
the default code is enumerated in the colour_hue list.
;
_name.category_id model_site
_name.object_id display_colour
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
_enumeration.def_index_id '_model_site.type_symbol'
loop_
_enumeration_set.state
_enumeration_set.detail
black '[ 000, 000, 000 ]'
white '[ 255, 255, 255 ]'
grey '[ 192, 192, 192 ]'
grey_light '[ 211, 211, 211 ]'
grey_slate '[ 112, 128, 144 ]'
blue '[ 000, 000, 255 ]'
blue_light '[ 176, 224, 230 ]'
blue_medium '[ 000, 000, 205 ]'
blue_dark '[ 025, 025, 112 ]'
blue_navy '[ 000, 000, 128 ]'
blue_royal '[ 065, 105, 225 ]'
blue_sky '[ 135, 206, 235 ]'
blue_steel '[ 070, 130, 180 ]'
turquoise '[ 064, 224, 208 ]'
cyan '[ 000, 255, 255 ]'
cyan_light '[ 224, 255, 255 ]'
green '[ 000, 255, 000 ]'
green_light '[ 152, 251, 152 ]'
green_dark '[ 000, 100, 000 ]'
green_sea '[ 046, 139, 087 ]'
green_lime '[ 050, 205, 050 ]'
green_olive '[ 107, 142, 035 ]'
green_khaki '[ 240, 230, 140 ]'
yellow '[ 255, 255, 000 ]'
yellow_light '[ 255, 255, 224 ]'
yellow_gold '[ 255, 215, 000 ]'
brown '[ 165, 042, 042 ]'
brown_sienna '[ 160, 082, 045 ]'
brown_beige '[ 245, 245, 220 ]'
brown_tan '[ 210, 180, 140 ]'
salmon '[ 250, 128, 114 ]'
salmon_light '[ 255, 160, 122 ]'
salmon_dark '[ 233, 150, 122 ]'
orange '[ 255, 165, 000 ]'
orange_dark '[ 255, 140, 000 ]'
red '[ 255, 000, 000 ]'
red_coral '[ 255, 127, 080 ]'
red_tomato '[ 255, 099, 071 ]'
red_orange '[ 255, 069, 000 ]'
red_violet '[ 219, 112, 147 ]'
red_maroon '[ 176, 048, 096 ]'
pink '[ 255, 192, 203 ]'
pink_light '[ 255, 182, 193 ]'
pink_deep '[ 255, 020, 147 ]'
pink_hot '[ 255, 105, 180 ]'
violet '[ 238, 130, 238 ]'
violet_red '[ 208, 032, 144 ]'
violet_magenta '[ 255, 000, 255 ]'
violet_dark '[ 148, 000, 211 ]'
violet_blue '[ 138, 043, 226 ]'
loop_
_enumeration_default.index
_enumeration_default.value
H white
D blue_light
H1- white
He unknown
Li unknown
Li1+ unknown
Be unknown
Be2+ unknown
B unknown
C steel_grey
N blue
O red
O1- red
F green
F1- green
Ne unknown
Na magenta
Na1+ magenta
Mg magenta
Mg2+ magenta
Al magenta
Al3+ magenta
Si unknown
Si4+ unknown
P magenta
S yellow
Cl green
Cl1- green
Ar unknown
K magenta
K1+ magenta
Ca magenta
Ca2+ magenta
Sc unknown
Sc3+ unknown
Ti magenta
Ti2+ magenta
Ti3+ magenta
Ti4+ magenta
V magenta
V2+ magenta
V3+ magenta
V5+ magenta
Cr magenta
Cr2+ magenta
Cr3+ magenta
Mn magenta
Mn2+ magenta
Mn3+ magenta
Mn4+ magenta
Fe magenta
Fe2+ magenta
Fe3+ magenta
Co magenta
Co2+ magenta
Co3+ magenta
Ni magenta
Ni2+ magenta
Ni3+ magenta
Cu magenta
Cu1+ magenta
Cu2+ magenta
Zn magenta
Zn2+ magenta
Ga magenta
Ga3+ magenta
Ge magenta
Ge4+ magenta
As magenta
Se yellow
Br green
Br1- green
Kr unknown
Rb unknown
Rb1+ unknown
Sr unknown
Sr2+ unknown
Y unknown
Y3+ unknown
Zr unknown
Zr4+ unknown
Nb unknown
Nb3+ unknown
Nb5+ unknown
Mo unknown
Mo3+ magenta
Mo5+ magenta
Mo6+ magenta
Tc unknown
Ru unknown
Ru3+ unknown
Ru4+ unknown
Rh unknown
Rh3+ unknown
Rh4+ unknown
Pd unknown
Pd2+ unknown
Pd4+ unknown
Ag magenta
Ag1+ magenta
Ag2+ magenta
Cd magenta
Cd2+ magenta
In unknown
In3+ unknown
Sn magenta
Sn2+ magenta
Sn4+ magenta
Sb magenta
Sb3+ magenta
Sb5+ magenta
Te unknown
I green
I1- green
Xe unknown
Cs unknown
Cs1+ unknown
Ba unknown
Ba2+ unknown
La unknown
La3+ unknown
Ce unknown
Ce3+ unknown
Ce4+ unknown
Pr unknown
Pr3+ unknown
Pr4+ unknown
Nd unknown
Nd3+ unknown
Pm unknown
Sm unknown
Sm3+ unknown
Eu unknown
Eu2+ unknown
Eu3+ unknown
Gd unknown
Gd3+ unknown
Tb unknown
Tb3+ unknown
Dy unknown
Dy3+ unknown
Ho unknown
Ho3+ unknown
Er unknown
Er3+ unknown
Tm unknown
Tm3+ unknown
Yb unknown
Yb2+ unknown
Yb3+ unknown
Lu unknown
Lu3+ unknown
Hf unknown
Hf4+ unknown
Ta unknown
Ta5+ unknown
W unknown
W6+ unknown
Re unknown
Os unknown
Os4+ unknown
Ir unknown
Ir3+ unknown
Ir4+ unknown
Pt magenta
Pt2+ magenta
Pt4+ magenta
Au magenta
Au1+ magenta
Au3+ magenta
Hg magenta
Hg1+ magenta
Hg2+ magenta
Tl unknown
TL1+ unknown
Tl3+ unknown
Pb magenta
Pb2+ magenta
Pb4+ magenta
Bi magenta
Bi3+ magenta
Bi5+ magenta
Po unknown
At unknown
Rn unknown
Fr unknown
Ra unknown
Ra2+ unknown
Ac unknown
Ac3+ unknown
Th unknown
Th4+ unknown
Pa unknown
U unknown
U3+ unknown
U4+ unknown
U6+ unknown
Np unknown
Np3+ unknown
Np4+ unknown
Np6+ unknown
Pu unknown
Pu3+ unknown
Pu4+ unknown
Pu6+ unknown
Am unknown
Cm unknown
Bk unknown
Cf unknown
save_
save__model_site.fract_xyz
_definition.id '_model_site.fract_xyz'
loop_
_alias.definition_id
'_model_site.fract_xyz'
_definition.update 2012-12-14
_description.text
;
Vector of fractional atom site coordinates.
;
_name.category_id model_site
_name.object_id fract_xyz
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With m as model_site
xyz = _atom_site[m.label].fract_xyz
_model_site.fract_xyz = SymEquiv(m.symop, xyz)
;
save_
save__model_site.id
_definition.id '_model_site.id'
loop_
_alias.definition_id
'_model_site.id'
_definition.update 2012-11-22
_description.text
;
Identifier of model site in terms of the atom site label and
symmetry operator.
;
_name.category_id model_site
_name.object_id id
_type.purpose Composite
_type.source Derived
_type.container List
_type.contents 'List(Code,Symop)'
_type.dimension [1]
loop_
_method.purpose
_method.expression
Evaluation
;
With m as model_site
_model_site.id = List ( m.label, m.symop )
;
save_
save__model_site.index
_definition.id '_model_site.index'
loop_
_alias.definition_id
'_model_site.index'
_definition.update 2012-11-22
_description.text
;
Index number of an atomic site in the connected molecule.
;
_name.category_id model_site
_name.object_id index
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Index
_enumeration.range 1:
save_
save__model_site.key
_definition.id '_model_site.key'
loop_
_alias.definition_id
'_model_site.key'
_definition.update 2012-11-22
_description.text
;
Value is a unique key to a set of MODEL_SITE items
in a looped list.
;
_name.category_id model_site
_name.object_id key
_type.purpose Key
_type.source Related
_type.container List
_type.contents 'List(Code,Symop)'
_type.dimension [1]
loop_
_method.purpose
_method.expression
Evaluation ' _model_site.key = _model_site.id'
save_
save__model_site.label
_definition.id '_model_site.label'
loop_
_alias.definition_id
'_model_site.label'
_definition.update 2012-11-22
_description.text
;
Code identifies a site in the atom_site category of data.
;
_name.category_id model_site
_name.object_id label
_name.linked_item_id '_atom_site.label'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation
;
_model_site.label = _model_site.id [0]
;
save_
save__model_site.mole_index
_definition.id '_model_site.mole_index'
loop_
_alias.definition_id
'_model_site.mole_index'
_definition.update 2013-03-09
_description.text
;
Index number of a distinct molecules in the cell, not related by
symmetry.
;
_name.category_id model_site
_name.object_id mole_index
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Index
save_
save__model_site.radius_bond
_definition.id '_model_site.radius_bond'
loop_
_alias.definition_id
'_model_site.radius_bond'
_definition.update 2012-11-22
_description.text
;
Atomic radius of atom located at this site.
;
_name.category_id model_site
_name.object_id radius_bond
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.1:
_units.code angstroms
loop_
_method.purpose
_method.expression
Evaluation
;
With m as model_site
_model_site.radius_bond = _atom_type[m.type_symbol].radius_bond
;
save_
save__model_site.radius_contact
_definition.id '_model_site.radius_contact'
loop_
_alias.definition_id
'_model_site.radius_contact'
_definition.update 2012-11-22
_description.text
;
Atomic contact radius of atom specie located at this site.
;
_name.category_id model_site
_name.object_id radius_contact
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 1.:
_units.code angstroms
loop_
_method.purpose
_method.expression
Evaluation
;
With m as model_site
_model_site.radius_contact = _atom_type[m.type_symbol].radius_contact
;
save_
save__model_site.symop
_definition.id '_model_site.symop'
loop_
_alias.definition_id
'_model_site.symop'
_name.category_id model_site
_name.object_id symop
loop_
_method.purpose
_method.expression
Evaluation
;
_model_site.symop = _model_site.id [1]
;
_type.contents Symop
_type.purpose Composite
_description.text
;
The set of data items which specify the symmetry operation codes
which must be applied to the atom sites involved in the geometry angle.
The symmetry code of each atom site as the symmetry-equivalent position
number 'n' and the cell translation number 'klm'. These numbers are
combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site.fract_xyz. It must match a
number given in _symmetry_equiv.pos_site_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
;
_enumeration.default 1_555
_type.source Derived
_type.container Single
_definition.update 2014-06-29
loop_
_description_example.case
_description_example.detail
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
. 'no symmetry or translation to site'
save_
save__model_site.type_symbol
_definition.id '_model_site.type_symbol'
loop_
_alias.definition_id
'_model_site.type_symbol'
_definition.update 2012-11-22
_description.text
;
Code to identify the atom specie(s) occupying this site.
;
_name.category_id model_site
_name.object_id type_symbol
_name.linked_item_id '_atom_type.symbol'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation
;
_model_site.type_symbol = AtomType ( _model_site.label )
;
save_
save_VALENCE
_definition.id VALENCE
_definition.scope Category
_definition.class Set
_definition.update 2012-12-13
_description.text
;
The CATEGORY of items used to specify bond valence parameters
used to calculate bond valences from bond lengths.
;
_name.category_id MODEL
_name.object_id VALENCE
save_
save_VALENCE_PARAM
_definition.id VALENCE_PARAM
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of items for listing bond valences.
;
_name.category_id VALENCE
_name.object_id VALENCE_PARAM
_category.key_id '_valence_param.key'
_category.key_list ['_valence_param.id']
save_
save__valence_param.atom_1
_definition.id '_valence_param.atom_1'
loop_
_alias.definition_id
'_valence_param.atom_1'
'_valence_param_atom_1'
_definition.update 2012-12-13
_description.text
;
Atom type symbol for atom 1 forming a bond whose
valence parameters are given in this category.
;
_name.category_id valence_param
_name.object_id atom_1
_name.linked_item_id '_atom_type.symbol'
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__valence_param.atom_1_valence
_definition.id '_valence_param.atom_1_valence'
loop_
_alias.definition_id
'_valence_param.atom_1_valence'
'_valence_param_atom_1_valence'
_definition.update 2012-12-13
_description.text
;
The valence (formal charge) of the atom 1 whose bond
valence parameters are given in this category.
;
_name.category_id valence_param
_name.object_id atom_1_valence
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code coulomb
save_
save__valence_param.atom_2
_definition.id '_valence_param.atom_2'
loop_
_alias.definition_id
'_valence_param.atom_2'
'_valence_param_atom_2'
_definition.update 2012-12-13
_description.text
;
Atom type symbol for atom 2 forming a bond whose
valence parameters are given in this category.
;
_name.category_id valence_param
_name.object_id atom_2
_name.linked_item_id '_atom_type.symbol'
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__valence_param.atom_2_valence
_definition.id '_valence_param.atom_2_valence'
loop_
_alias.definition_id
'_valence_param.atom_2_valence'
'_valence_param_atom_2_valence'
_definition.update 2012-12-13
_description.text
;
The valence (formal charge) of the atom 2 whose bond
valence parameters are given in this category.
;
_name.category_id valence_param
_name.object_id atom_2_valence
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code coulomb
save_
save__valence_param.B
_definition.id '_valence_param.B'
loop_
_alias.definition_id
'_valence_param.B'
'_valence_param_B'
_definition.update 2012-12-13
_description.text
;
The bond valence parameter B used in the expression
s = exp[(Ro - R)/B] where s is the valence of bond length R.
;
_name.category_id valence_param
_name.object_id B
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.1:
_units.code Angstroms
save_
save__valence_param.details
_definition.id '_valence_param.details'
loop_
_alias.definition_id
'_valence_param.details'
'_valence_param_details'
_definition.update 2012-12-13
_description.text
;
Details of valence parameters of stated bond.
;
_name.category_id valence_param
_name.object_id details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__valence_param.id
_definition.id '_valence_param.id'
loop_
_alias.definition_id
'_valence_param.id'
'_valence_param_id'
_definition.update 2012-12-13
_description.text
;
Unique index loop number of the valence parameter loop.
;
_name.category_id valence_param
_name.object_id id
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Index
_enumeration.range 1:
save_
save__valence_param.key
_definition.id '_valence_param.key'
loop_
_alias.definition_id
'_valence_param.key'
_definition.update 2012-12-13
_description.text
;
Unique key to looped list of VALENCE_PARAM items.
;
_name.category_id valence_param
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Index
loop_
_method.purpose
_method.expression
Evaluation ' _valence_param.key = _valence_param.id'
save_
save__valence_param.ref_id
_definition.id '_valence_param.ref_id'
loop_
_alias.definition_id
'_valence_param.ref_id'
'_valence_param_ref_id'
_definition.update 2012-12-13
_description.text
;
Code linking parameters to the key valence_ref.id key
in the reference list in category VALENCE_REF.
;
_name.category_id valence_param
_name.object_id ref_id
_name.linked_item_id '_valence_ref.id'
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__valence_param.Ro
_definition.id '_valence_param.Ro'
loop_
_alias.definition_id
'_valence_param.Ro'
'_valence_param_Ro'
_definition.update 2012-12-13
_description.text
;
The bond valence parameter Ro used in the expression
s = exp[(Ro - R)/B] where s is the valence of bond length R.
;
_name.category_id valence_param
_name.object_id Ro
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 1.:
_units.code Angstroms
save_
save_VALENCE_REF
_definition.id VALENCE_REF
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of items for listing valence references.
;
_name.category_id VALENCE
_name.object_id VALENCE_REF
_category.key_id '_valence_ref.key'
_category.key_list ['_valence_ref.id']
save_
save__valence_ref.id
_definition.id '_valence_ref.id'
loop_
_alias.definition_id
'_valence_ref.id'
'_valence_ref_id'
_definition.update 2012-12-13
_description.text
;
Unique loop code of the valence references.
;
_name.category_id valence_ref
_name.object_id id
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__valence_ref.key
_definition.id '_valence_ref.key'
loop_
_alias.definition_id
'_valence_ref.key'
_definition.update 2012-12-13
_description.text
;
Unique key to looped list of VALENCE_REF items.
;
_name.category_id valence_ref
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _valence_ref.key = _valence_ref.id'
save_
save__valence_ref.reference
_definition.id '_valence_ref.reference'
loop_
_alias.definition_id
'_valence_ref.reference'
'_valence_ref_reference'
_definition.update 2012-12-13
_description.text
;
Literature reference from which the valence parameters
identified by _valence_param.id were taken
;
_name.category_id valence_ref
_name.object_id reference
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_PUBLICATION
_definition.id PUBLICATION
_definition.scope Category
_definition.class Set
_definition.update 2015-09-04
_description.text
;
The DICTIONARY group encompassing the CORE PUBLICATION data items defined
and used with in the Crystallographic Information Framework (CIF).
;
_name.category_id CIF_CORE
_name.object_id PUBLICATION
save_
save_AUDIT
_definition.id AUDIT
_definition.scope Category
_definition.class Set
_definition.update 2012-05-07
_description.text
;
The CATEGORY of data items used to record details about the
creation and subsequent updating of the data block.
;
_name.category_id PUBLICATION
_name.object_id AUDIT
save_
save__audit.block_code
_definition.id '_audit.block_code'
loop_
_alias.definition_id
'_audit.block_code'
'_audit_block_code'
'_audit.revision_id'
_definition.update 2013-04-10
_description.text
;
A unique block_code identifier for each revision.
;
_name.category_id audit
_name.object_id block_code
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
loop_
_description_example.case
TOZ_1991-03-20
save_
save__audit.creation_date
_definition.id '_audit.creation_date'
loop_
_alias.definition_id
'_audit.creation_date'
'_audit_creation_date'
_definition.update 2012-11-29
_description.text
;
The date dd-mm-yyyy of each revision to the data.
;
_name.category_id audit
_name.object_id creation_date
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Date
loop_
_description_example.case
1991-03-20
save_
save__audit.creation_method
_definition.id '_audit.creation_method'
loop_
_alias.definition_id
'_audit.creation_method'
'_audit_creation_method'
_definition.update 2012-11-29
_description.text
;
A description of how the revision was applied to the data.
;
_name.category_id audit
_name.object_id creation_method
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'spawned by the program QBEE'
save_
save__audit.update_record
_definition.id '_audit.update_record'
loop_
_alias.definition_id
'_audit.update_record'
'_audit_update_record'
_definition.update 2012-11-29
_description.text
;
A description of the revision applied to the data.
;
_name.category_id audit
_name.object_id update_record
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'1990-07-15 Updated by Co-editor'
save_
save_AUDIT_AUTHOR
_definition.id AUDIT_AUTHOR
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used for author(s) details.
;
_name.category_id AUDIT
_name.object_id AUDIT_AUTHOR
_category.key_id '_audit_author.key'
_category.key_list ['_audit_author.name']
save_
save__audit_author.address
_definition.id '_audit_author.address'
loop_
_alias.definition_id
'_audit_author.address'
'_audit_author_address'
_definition.update 2012-11-29
_description.text
;
The address of an author of this data block. If there are
multiple authors, _audit_author_address is looped with
_audit_author.name.
;
_name.category_id audit_author
_name.object_id address
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
;Department
Institute
Street
City and postcode
COUNTRY
;
save_
save__audit_author.key
_definition.id '_audit_author.key'
loop_
_alias.definition_id
'_audit_author.key'
_definition.update 2012-12-13
_description.text
;
Value is a unique key to a set of AUDIT_AUTHOR items
in a looped list.
;
_name.category_id audit_author
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Text
loop_
_method.purpose
_method.expression
Evaluation ' _audit_author.key = _audit_author.name'
save_
save__audit_author.name
_definition.id '_audit_author.name'
loop_
_alias.definition_id
'_audit_author.name'
'_audit_author_name'
_definition.update 2012-11-29
_description.text
;
The name of an author of this data block. If there are multiple
authors, _audit_author.name is looped with _audit_author.address.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
;
_name.category_id audit_author
_name.object_id name
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A.'
'M\"uller, H.A.'
'Ross II, C.R.'
save_
save_AUDIT_CONFORM
_definition.id AUDIT_CONFORM
_definition.scope Category
_definition.class Set
_definition.update 2012-05-07
_description.text
;
The CATEGORY of data items used describe dictionary versions
by which data names in the current data block are conformant.
;
_name.category_id AUDIT
_name.object_id AUDIT_CONFORM
save_
save__audit_conform.dict_location
_definition.id '_audit_conform.dict_location'
loop_
_alias.definition_id
'_audit_conform.dict_location'
'_audit_conform_dict_location'
_definition.update 2012-11-29
_description.text
;
File name or uniform resource locator (URL) where the
conformant data dictionary resides.
;
_name.category_id audit_conform
_name.object_id dict_location
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__audit_conform.dict_name
_definition.id '_audit_conform.dict_name'
loop_
_alias.definition_id
'_audit_conform.dict_name'
'_audit_conform_dict_name'
_definition.update 2012-11-29
_description.text
;
Name identifying highest-level data dictionary defining
data names used in this file.
;
_name.category_id audit_conform
_name.object_id dict_name
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__audit_conform.dict_version
_definition.id '_audit_conform.dict_version'
loop_
_alias.definition_id
'_audit_conform.dict_version'
'_audit_conform_dict_version'
_definition.update 2012-11-29
_description.text
;
Code for the version of data dictionary defining data names
used in this file.
;
_name.category_id audit_conform
_name.object_id dict_version
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save_AUDIT_CONTACT_AUTHOR
_definition.id AUDIT_CONTACT_AUTHOR
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used for contact author(s) details.
;
_name.category_id AUDIT
_name.object_id AUDIT_CONTACT_AUTHOR
_category.key_id '_audit_contact_author.key'
_category.key_list ['_audit_contact_author.name']
save_
save__audit_contact_author.address
_definition.id '_audit_contact_author.address'
loop_
_alias.definition_id
'_audit_contact_author.address'
'_audit_contact_author_address'
_definition.update 2012-11-29
_description.text
;
The mailing address of the author of the data block to whom
correspondence should be addressed.
;
_name.category_id audit_contact_author
_name.object_id address
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
; Department
Institute
Street
City and postcode
COUNTRY
;
save_
save__audit_contact_author.email
_definition.id '_audit_contact_author.email'
loop_
_alias.definition_id
'_audit_contact_author.email'
'_audit_contact_author_email'
_definition.update 2012-11-29
_description.text
;
The electronic mail address of the author of the data block
to whom correspondence should be addressed, in a form
recognizable to international networks. The format of e-mail
addresses is given in Section 3.4, Address Specification, of
Internet Message Format, RFC 2822, P. Resnick (Editor),
Network Standards Group, April 2001.
;
_name.category_id audit_contact_author
_name.object_id email
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
name@host.domain.country
bm@iucr.org
save_
save__audit_contact_author.fax
_definition.id '_audit_contact_author.fax'
loop_
_alias.definition_id
'_audit_contact_author.fax'
'_audit_contact_author_fax'
_definition.update 2012-11-29
_description.text
;
Facsimile telephone number of the author submitting the manuscript
and data block.
The recommended style is the international dialing prefix, followed
by the area code in parentheses, followed by the local number with
no spaces. The earlier convention of including the international
dialing prefix in parentheses is no longer recommended.
;
_name.category_id audit_contact_author
_name.object_id fax
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
12(34)9477334
12()349477334
save_
save__audit_contact_author.key
_definition.id '_audit_contact_author.key'
loop_
_alias.definition_id
'_audit_contact_author.key'
_definition.update 2012-12-13
_description.text
;
Value is a unique key to a set of AUDIT_CONTACT_AUTHOR items
in a looped list.
;
_name.category_id audit_contact_author
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Text
loop_
_method.purpose
_method.expression
Evaluation ' _audit_contact_author.key = _audit_contact_author.name'
save_
save__audit_contact_author.name
_definition.id '_audit_contact_author.name'
loop_
_alias.definition_id
'_audit_contact_author.name'
'_audit_contact_author_name'
'_audit_contact_author'
_definition.update 2012-11-29
_description.text
;
The name of the author of the data block to whom correspondence
should be addressed. The family name(s), followed by a comma and
including any dynastic components, precedes the first name(s) or
initial(s).
;
_name.category_id audit_contact_author
_name.object_id name
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
save_
save__audit_contact_author.phone
_definition.id '_audit_contact_author.phone'
loop_
_alias.definition_id
'_audit_contact_author.phone'
'_audit_contact_author_phone'
_definition.update 2012-11-29
_description.text
;
Telephone number of author submitting the manuscript and data block.
The recommended style is the international dialing prefix,
followed by the area code in parentheses, followed by the
local number and any extension number prefixed by 'x', with
no spaces. The earlier convention of including the international
dialing prefix in parentheses is no longer recommended.
;
_name.category_id audit_contact_author
_name.object_id phone
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
12(34)9477330
12()349477330
12(34)9477330x5543
save_
save_AUDIT_LINK
_definition.id AUDIT_LINK
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to record details about the
relationships between data blocks in the current CIF.
;
_name.category_id AUDIT
_name.object_id AUDIT_LINK
_category.key_id '_audit_link.key'
_category.key_list ['_audit_link.block_code']
save_
save__audit_link.block_code
_definition.id '_audit_link.block_code'
loop_
_alias.definition_id
'_audit_link.block_code'
'_audit_link_block_code'
_definition.update 2013-04-18
_description.text
;
The value of _audit.block_code associated with a data block
in the current file related to the current data block. The
special value '.' may be used to refer to the current data
block for completeness.
;
_name.category_id audit_link
_name.object_id block_code
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save__audit_link.block_description
_definition.id '_audit_link.block_description'
loop_
_alias.definition_id
'_audit_link.block_description'
'_audit_link_block_description'
_definition.update 2012-11-29
_description.text
;
Description of the relationship of the referenced data block
to the current one.
;
_name.category_id audit_link
_name.object_id block_description
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__audit_link.key
_definition.id '_audit_link.key'
loop_
_alias.definition_id
'_audit_link.key'
_definition.update 2012-12-13
_description.text
;
Value is a unique key to a set of AUDIT_LINK items
in a looped list.
;
_name.category_id audit_link
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _audit_link.key = _audit_link.block_code'
save_
save_CITATION
_definition.id CITATION
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
Category of items describing literature cited in the publication.
;
_name.category_id PUBLICATION
_name.object_id CITATION
_category.key_id '_citation.key'
_category.key_list ['_citation.id']
save_
save__citation.abstract
_definition.id '_citation.abstract'
loop_
_alias.definition_id
'_citation.abstract'
'_citation_abstract'
_definition.update 2012-12-11
_description.text
;
Abstract for the citation. This is used most when the
citation is extracted from a bibliographic database that
contains full text or abstract information.
;
_name.category_id citation
_name.object_id abstract
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__citation.abstract_id_CAS
_definition.id '_citation.abstract_id_CAS'
loop_
_alias.definition_id
'_citation.abstract_id_CAS'
'_citation_abstract_id_CAS'
_definition.update 2012-12-11
_description.text
;
Chemical Abstracts Service (CAS) abstract identifier.
;
_name.category_id citation
_name.object_id abstract_id_CAS
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__citation.book_id_ISBN
_definition.id '_citation.book_id_ISBN'
loop_
_alias.definition_id
'_citation.book_id_ISBN'
'_citation_book_id_ISBN'
_definition.update 2012-12-11
_description.text
;
International Standard Book Number (ISBN) for book chap. cited.
;
_name.category_id citation
_name.object_id book_id_ISBN
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__citation.book_publisher
_definition.id '_citation.book_publisher'
loop_
_alias.definition_id
'_citation.book_publisher'
'_citation_book_publisher'
_definition.update 2012-12-11
_description.text
;
Publisher of the citation; relevant for book chapters.
;
_name.category_id citation
_name.object_id book_publisher
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__citation.book_publisher_city
_definition.id '_citation.book_publisher_city'
loop_
_alias.definition_id
'_citation.book_publisher_city'
'_citation_book_publisher_city'
_definition.update 2012-12-11
_description.text
;
Location of publisher of the citation; relevant for book chapters.
;
_name.category_id citation
_name.object_id book_publisher_city
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__citation.book_title
_definition.id '_citation.book_title'
loop_
_alias.definition_id
'_citation.book_title'
'_citation_book_title'
_definition.update 2012-12-11
_description.text
;
Title of the book in which the citation appeared.
;
_name.category_id citation
_name.object_id book_title
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__citation.coordinate_linkage
_definition.id '_citation.coordinate_linkage'
loop_
_alias.definition_id
'_citation.coordinate_linkage'
'_citation_coordinate_linkage'
_definition.update 2012-12-11
_description.text
;
Code specifies whether this citation is concerned with precisely
the set of coordinates given in the data block. If, for instance,
the publication described the same structure, but the coordinates
had undergone further refinement prior to creation of the data
block, the value of this data item would be 'no'.
;
_name.category_id citation
_name.object_id coordinate_linkage
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
no 'citation unrelated to current coordinates'
n 'abbreviation for "no"'
yes 'citation related to current coordinates'
y 'abbreviation for "yes"'
_enumeration.default yes
save_
save__citation.country
_definition.id '_citation.country'
loop_
_alias.definition_id
'_citation.country'
'_citation_country'
_definition.update 2012-12-11
_description.text
;
Country of publication; for journal articles and book chapters.
;
_name.category_id citation
_name.object_id country
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__citation.database_id_CSD
_definition.id '_citation.database_id_CSD'
loop_
_alias.definition_id
'_citation.database_id_CSD'
'_citation_database_id_CSD'
_definition.update 2012-12-11
_description.text
;
Identifier ('refcode') of the database record in the Cambridge
Structural Database containing details of the cited structure.
;
_name.category_id citation
_name.object_id 'database_id_CSD'
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save__citation.database_id_Medline
_definition.id '_citation.database_id_Medline'
loop_
_alias.definition_id
'_citation.database_id_Medline'
'_citation_database_id_Medline'
_definition.update 2012-12-11
_description.text
;
i Medline accession number categorizing a bibliographic entry.
;
_name.category_id citation
_name.object_id 'database_id_Medline'
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save__citation.id
_definition.id '_citation.id'
loop_
_alias.definition_id
'_citation.id'
'_citation_id'
_definition.update 2012-12-11
_description.text
;
Unique identifier to the CITATION list. A value of 'primary'
should be used to indicate the citation that the author(s)
consider to be the most pertinent to the contents of the data
block. Note that this item need not be a number; it can be
any unique identifier.
;
_name.category_id citation
_name.object_id id
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
loop_
_description_example.case
primary
1
2
3
save_
save__citation.journal_abbrev
_definition.id '_citation.journal_abbrev'
loop_
_alias.definition_id
'_citation.journal_abbrev'
'_citation_journal_abbrev'
_definition.update 2012-12-11
_description.text
;
Abbreviated name of the journal cited as given in the Chemical
Abstracts Service Source Index.
;
_name.category_id citation
_name.object_id journal_abbrev
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'J. Mol. Biol.'
save_
save__citation.journal_full
_definition.id '_citation.journal_full'
loop_
_alias.definition_id
'_citation.journal_full'
'_citation_journal_full'
_definition.update 2012-12-11
_description.text
;
Full name of the journal cited; relevant for journal articles.
;
_name.category_id citation
_name.object_id journal_full
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'Journal of Molecular Biology'
save_
save__citation.journal_id_ASTM
_definition.id '_citation.journal_id_ASTM'
loop_
_alias.definition_id
'_citation.journal_id_ASTM'
'_citation_journal_id_ASTM'
_definition.update 2012-12-11
_description.text
;
American Society for the Testing of Materials (ASTM) code assigned
to the journal cited (also referred to as the CODEN designator of
the Chemical Abstracts Service); relevant for journal articles.
;
_name.category_id citation
_name.object_id journal_id_ASTM
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save__citation.journal_id_CSD
_definition.id '_citation.journal_id_CSD'
loop_
_alias.definition_id
'_citation.journal_id_CSD'
'_citation_journal_id_CSD'
_definition.update 2012-12-11
_description.text
;
The Cambridge Structural Database (CSD) code assigned to the
journal cited; relevant for journal articles. This is also the
system used at the Protein Data Bank (PDB).
;
_name.category_id citation
_name.object_id journal_id_CSD
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
loop_
_description_example.case
0070
save_
save__citation.journal_id_ISSN
_definition.id '_citation.journal_id_ISSN'
loop_
_alias.definition_id
'_citation.journal_id_ISSN'
'_citation_journal_id_ISSN'
_definition.update 2012-12-11
_description.text
;
The International Standard Serial Number (ISSN) code assigned to
the journal cited; relevant for journal articles.
;
_name.category_id citation
_name.object_id journal_id_ISSN
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save__citation.journal_issue
_definition.id '_citation.journal_issue'
loop_
_alias.definition_id
'_citation.journal_issue'
'_citation_journal_issue'
_definition.update 2012-12-11
_description.text
;
Issue number of the journal cited; relevant for articles.
;
_name.category_id citation
_name.object_id journal_issue
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Index
_enumeration.range 1:
loop_
_description_example.case
2
save_
save__citation.journal_volume
_definition.id '_citation.journal_volume'
loop_
_alias.definition_id
'_citation.journal_volume'
'_citation_journal_volume'
_definition.update 2012-12-11
_description.text
;
Volume number of the journal cited; relevant for articles.
;
_name.category_id citation
_name.object_id journal_volume
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Index
_enumeration.range 1:
loop_
_description_example.case
174
save_
save__citation.key
_definition.id '_citation.key'
loop_
_alias.definition_id
'_citation.key'
_definition.update 2012-12-13
_description.text
;
Value is a unique key to a set of CITATION items
in a looped list.
;
_name.category_id citation
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _citation.key = _citation.id'
save_
save__citation.language
_definition.id '_citation.language'
loop_
_alias.definition_id
'_citation.language'
'_citation_language'
_definition.update 2012-12-11
_description.text
;
Language in which the citation appears.
;
_name.category_id citation
_name.object_id language
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
German
save_
save__citation.page_first
_definition.id '_citation.page_first'
loop_
_alias.definition_id
'_citation.page_first'
'_citation_page_first'
_definition.update 2012-12-11
_description.text
;
First page of citation; relevant for articles and book chapters.
;
_name.category_id citation
_name.object_id page_first
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Index
_enumeration.range 1:
save_
save__citation.page_last
_definition.id '_citation.page_last'
loop_
_alias.definition_id
'_citation.page_last'
'_citation_page_last'
_definition.update 2012-12-11
_description.text
;
Last page of citation; relevant for articles and book chapters.
;
_name.category_id citation
_name.object_id page_last
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Index
_enumeration.range 1:
save_
save__citation.special_details
_definition.id '_citation.special_details'
loop_
_alias.definition_id
'_citation.special_details'
'_citation_special_details'
'_citation.details'
_definition.update 2012-12-11
_description.text
;
Special aspects of the relationship of the data block contents
to the literature item cited.
;
_name.category_id citation
_name.object_id special_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__citation.title
_definition.id '_citation.title'
loop_
_alias.definition_id
'_citation.title'
'_citation_title'
_definition.update 2012-12-11
_description.text
;
Title of citation; relevant for articles and book chapters.
;
_name.category_id citation
_name.object_id title
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__citation.year
_definition.id '_citation.year'
loop_
_alias.definition_id
'_citation.year'
'_citation_year'
_definition.update 2012-12-11
_description.text
;
Year of citation; relevant for articles and book chapters.
;
_name.category_id citation
_name.object_id year
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_CITATION_AUTHOR
_definition.id CITATION_AUTHOR
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
Category of items describing citation author(s) details.
;
_name.category_id PUBLICATION
_name.object_id CITATION_AUTHOR
_category.key_id '_citation_author.key'
_category.key_list ['_citation_author.ordinal']
save_
save__citation_author.citation_id
_definition.id '_citation_author.citation_id'
loop_
_alias.definition_id
'_citation_author.citation_id'
'_citation_author_citation_id'
_definition.update 2012-12-11
_description.text
;
Code identifier in the CITATION data list. The value of must match
an identifier specified in the CITATION list.
;
_name.category_id citation_author
_name.object_id citation_id
_name.linked_item_id '_citation.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save__citation_author.key
_definition.id '_citation_author.key'
loop_
_alias.definition_id
'_citation_author.key'
_definition.update 2012-12-13
_description.text
;
Value is a unique key to a set of CITATION_AUTHOR items
in a looped list.
;
_name.category_id citation_author
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _citation_author.key = _citation_author.ordinal'
save_
save__citation_author.name
_definition.id '_citation_author.name'
loop_
_alias.definition_id
'_citation_author.name'
'_citation_author_name'
_definition.update 2012-12-11
_description.text
;
Name of citation author; relevant for articles and book chapters.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
;
_name.category_id citation_author
_name.object_id name
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A'
'M\"uller, H.A.'
'Ross II, C.R.'
save_
save__citation_author.ordinal
_definition.id '_citation_author.ordinal'
loop_
_alias.definition_id
'_citation_author.ordinal'
'_citation_author_ordinal'
_definition.update 2012-12-11
_description.text
;
Ordinal code specifies the order of the author's name in the list
of authors of the citation.
;
_name.category_id citation_author
_name.object_id ordinal
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save_CITATION_EDITOR
_definition.id CITATION_EDITOR
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
Category of items describing citation editor(s) details.
;
_name.category_id PUBLICATION
_name.object_id CITATION_EDITOR
_category.key_id '_citation_editor.key'
_category.key_list ['_citation_editor.id']
save_
save__citation_editor.citation_id
_definition.id '_citation_editor.citation_id'
loop_
_alias.definition_id
'_citation_editor.citation_id'
'_citation_editor_citation_id'
_definition.update 2012-12-11
_description.text
;
Code identifier in the CITATION list. The value must match an
identifier specified by _citation.id in the CITATION list.
;
_name.category_id citation_editor
_name.object_id citation_id
_name.linked_item_id '_citation.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save__citation_editor.id
_definition.id '_citation_editor.id'
loop_
_alias.definition_id
'_citation_editor.id'
_definition.update 2012-12-11
_description.text
;
Index number identifier of the CITATION_EDITOR category.
;
_name.category_id citation_editor
_name.object_id id
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Index
_enumeration.range 1:
save_
save__citation_editor.key
_definition.id '_citation_editor.key'
loop_
_alias.definition_id
'_citation_editor.key'
_definition.update 2012-12-13
_description.text
;
Value is a unique key to a set of CITATION_EDITOR items
in a looped list.
;
_name.category_id citation_editor
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Index
loop_
_method.purpose
_method.expression
Evaluation ' _citation_editor.key = _citation_editor.id'
save_
save__citation_editor.name
_definition.id '_citation_editor.name'
loop_
_alias.definition_id
'_citation_editor.name'
'_citation_editor'
'_citation_editor_name'
_definition.update 2012-12-11
_description.text
;
Name of citation editor; relevant for book chapters.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
;
_name.category_id citation_editor
_name.object_id name
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A'
'M\"uller, H.A.'
'Ross II, C.R.'
save_
save__citation_editor.ordinal
_definition.id '_citation_editor.ordinal'
loop_
_alias.definition_id
'_citation_editor.ordinal'
'_citation_editor_ordinal'
_definition.update 2014-06-12
_description.text
;
This data item defines the order of the editor's name in the
list of editors of a citation.
;
_name.category_id citation_editor
_name.object_id ordinal
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
save_
save_COMPUTING
_definition.id COMPUTING
_definition.scope Category
_definition.class Set
_definition.update 2012-05-07
_description.text
;
The CATEGORY of data items used to record details of the
computer programs used in the crystal structure analysis.
;
_name.category_id PUBLICATION
_name.object_id COMPUTING
save_
save__computing.cell_refinement
_definition.id '_computing.cell_refinement'
loop_
_alias.definition_id
'_computing.cell_refinement'
'_computing_cell_refinement'
_definition.update 2012-11-29
_description.text
;
Brief description of software used for cell_refinement.
;
_name.category_id computing
_name.object_id cell_refinement
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'CAD-4 (Enraf-Nonius, 1989)'
save_
save__computing.diffrn_collection
_definition.id '_computing.diffrn_collection'
loop_
_alias.definition_id
'_computing.diffrn_collection'
'_computing_data_collection'
'_computing.data_collection'
_definition.update 2012-12-11
_description.text
;
Description of software used to measure diffraction data.
;
_name.category_id computing
_name.object_id diffrn_collection
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'CAD-4 (Enraf-Nonius, 1989)'
save_
save__computing.diffrn_reduction
_definition.id '_computing.diffrn_reduction'
loop_
_alias.definition_id
'_computing.diffrn_reduction'
'_computing_data_reduction'
'_computing.data_reduction'
_definition.update 2012-12-11
_description.text
;
Description of software used to convert diffraction data
to measured structure factors.
;
_name.category_id computing
_name.object_id diffrn_reduction
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990)'
save_
save__computing.molecular_graphics
_definition.id '_computing.molecular_graphics'
loop_
_alias.definition_id
'_computing.molecular_graphics'
'_computing_molecular_graphics'
_definition.update 2012-11-29
_description.text
;
Brief description of software used for molecular_graphics.
;
_name.category_id computing
_name.object_id molecular_graphics
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__computing.publication_material
_definition.id '_computing.publication_material'
loop_
_alias.definition_id
'_computing.publication_material'
'_computing_publication_material'
_definition.update 2012-11-29
_description.text
;
Brief description of software used for publication_material.
;
_name.category_id computing
_name.object_id publication_material
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__computing.structure_refinement
_definition.id '_computing.structure_refinement'
loop_
_alias.definition_id
'_computing.structure_refinement'
'_computing_structure_refinement'
_definition.update 2012-11-29
_description.text
;
Brief description of software used for structure_refinement.
;
_name.category_id computing
_name.object_id structure_refinement
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'SHELXL93 (Sheldrick, 1993)'
save_
save__computing.structure_solution
_definition.id '_computing.structure_solution'
loop_
_alias.definition_id
'_computing.structure_solution'
'_computing_structure_solution'
_definition.update 2012-11-29
_description.text
;
Brief description of software used for structure_solution.
;
_name.category_id computing
_name.object_id structure_solution
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'SHELXS86 (Sheldrick, 1990)'
save_
save_DATABASE
_definition.id 'DATABASE'
_definition.scope Category
_definition.class Set
_definition.update 2012-12-13
_description.text
;
The CATEGORY of data items recording database deposition.
;
_name.category_id PUBLICATION
_name.object_id 'DATABASE'
save_
save__database.CSD_history
_definition.id '_database.CSD_history'
loop_
_alias.definition_id
'_database.CSD_history'
'_database_CSD_history'
_definition.update 2012-12-13
_description.text
;
The history of changes made by the Cambridge Crystallographic Data
Centre and incorporated into the Cambridge Structural Database (CSD).
;
_name.category_id 'database'
_name.object_id CSD_history
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__database.journal_ASTM
_definition.id '_database.journal_ASTM'
loop_
_alias.definition_id
'_database.journal_ASTM'
'_database_journal_ASTM'
_definition.update 2012-12-13
_description.text
;
ASTM CODEN designator for a journal as given in the Chemical
Source List maintained by the Chemical Abstracts Service.
;
_name.category_id 'database'
_name.object_id journal_ASTM
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save__database.journal_CSD
_definition.id '_database.journal_CSD'
loop_
_alias.definition_id
'_database.journal_CSD'
'_database_journal_CSD'
_definition.update 2012-12-13
_description.text
;
The journal code used in the Cambridge Structural Database.
;
_name.category_id 'database'
_name.object_id journal_CSD
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save_DATABASE_CODE
_definition.id 'DATABASE_CODE'
_definition.scope Category
_definition.class Set
_definition.update 2012-12-13
_description.text
;
The CATEGORY of data items recording database deposition. These data items
are assigned by database managers and should only appear in a CIF if they
originate from that source.
;
_name.category_id 'DATABASE'
_name.object_id 'DATABASE_CODE'
save_
save__database_code.CAS
_definition.id '_database_code.CAS'
loop_
_alias.definition_id
'_database_code.CAS'
'_database_code_CAS'
'_database.code_CAS'
_definition.update 2012-12-13
_description.text
;
Code assigned by the Chemical Abstracts Service.
;
_name.category_id 'database_code'
_name.object_id CAS
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__database_code.COD
_definition.id '_database_code.COD'
loop_
_alias.definition_id
'_database_code.COD'
'_database_code_COD'
'_database.code_COD'
_definition.update 2012-12-13
_description.text
;
Code assigned by Crystallography Open Database (COD).
;
_name.category_id 'database_code'
_name.object_id COD
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__database_code.CSD
_definition.id '_database_code.CSD'
loop_
_alias.definition_id
'_database_code.CSD'
'_database_code_CSD'
'_database.code_CSD'
_definition.update 2012-12-13
_description.text
;
Code assigned by the Cambridge Structural Database.
;
_name.category_id 'database_code'
_name.object_id CSD
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__database_code.depnum_ccdc_archive
_definition.id '_database_code.depnum_ccdc_archive'
loop_
_alias.definition_id
'_database_code.depnum_ccdc_archive'
'_database_code_depnum_ccdc_archive'
'_database.code_depnum_ccdc_archive'
_definition.update 2013-01-22
_description.text
;
Deposition numbers assigned by the Cambridge Crystallographic
Data Centre (CCDC) to files containing structural information
archived by the CCDC.
;
_name.category_id 'database_code'
_name.object_id depnum_ccdc_archive
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__database_code.depnum_ccdc_fiz
_definition.id '_database_code.depnum_ccdc_fiz'
loop_
_alias.definition_id
'_database_code.depnum_ccdc_fiz'
'_database_code_depnum_ccdc_fiz'
'_database.code_depnum_ccdc_fiz'
_definition.update 2013-01-22
_description.text
;
Deposition numbers assigned by the Fachinformationszentrum
Karlsruhe (FIZ) to files containing structural information
archived by the Cambridge Crystallographic Data Centre (CCDC).
;
_name.category_id 'database_code'
_name.object_id depnum_ccdc_fiz
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__database_code.depnum_ccdc_journal
_definition.id '_database_code.depnum_ccdc_journal'
loop_
_alias.definition_id
'_database_code.depnum_ccdc_journal'
'_database_code_depnum_ccdc_journal'
'_database.code_depnum_ccdc_journal'
_definition.update 2013-01-22
_description.text
;
Deposition numbers assigned by various journals to files
containing structural information archived by the Cambridge
Crystallographic Data Centre (CCDC).
;
_name.category_id 'database_code'
_name.object_id depnum_ccdc_journal
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__database_code.ICSD
_definition.id '_database_code.ICSD'
loop_
_alias.definition_id
'_database_code.ICSD'
'_database_code_ICSD'
'_database.code_ICSD'
_definition.update 2012-12-13
_description.text
;
Code assigned by the Inorganic Crystal Structure Database.
;
_name.category_id 'database_code'
_name.object_id ICSD
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__database_code.MDF
_definition.id '_database_code.MDF'
loop_
_alias.definition_id
'_database_code.MDF'
'_database_code_MDF'
'_database.code_MDF'
_definition.update 2012-12-13
_description.text
;
Code assigned in the Metals Data File.
;
_name.category_id 'database_code'
_name.object_id MDF
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save__database_code.NBS
_definition.id '_database_code.NBS'
loop_
_alias.definition_id
'_database_code.NBS'
'_database_code_NBS'
'_database.code_NBS'
_definition.update 2012-12-13
_description.text
;
Code assigned by the NBS (NIST) Crystal Data Database.
;
_name.category_id 'database_code'
_name.object_id NBS
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__database_code.PDB
_definition.id '_database_code.PDB'
loop_
_alias.definition_id
'_database_code.PDB'
'_database_code_PDB'
'_database.code_PDB'
_definition.update 2012-12-13
_description.text
;
Code assigned by the Protein Data Base.
;
_name.category_id 'database_code'
_name.object_id PDB
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__database_code.PDF
_definition.id '_database_code.PDF'
loop_
_alias.definition_id
'_database_code.PDF'
'_database_code_PDF'
'_database.code_PDF'
_definition.update 2012-12-13
_description.text
;
Code assigned in the Powder Diffraction File.
;
_name.category_id 'database_code'
_name.object_id PDF
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save_DISPLAY
_definition.id DISPLAY
_definition.scope Category
_definition.class Set
_definition.update 2012-05-07
_description.text
;
The CATEGORY of data items used to enumerate the display
parameters used in the discipline.
;
_name.category_id PUBLICATION
_name.object_id DISPLAY
save_
save_DISPLAY_COLOUR
_definition.id DISPLAY_COLOUR
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to enumerate the display
colour codes used in the discipline.
;
_name.category_id DISPLAY
_name.object_id DISPLAY_COLOUR
_category.key_id '_display_colour.key'
_category.key_list ['_display_colour.hue']
save_
save__display_colour.blue
_definition.id '_display_colour.blue'
loop_
_alias.definition_id
'_display_colour.blue'
_name.category_id display_colour
_name.object_id blue
_type.contents Index
_type.purpose Number
_description.text
;
Integer value between 0 and 255 giving the intensity of a
specific colour component (red, green or blue) for the RBG
display colour code.
;
_enumeration.range 0:255
_type.source Recorded
_type.container Single
_definition.update 2012-10-16
_units.code none
save_
save__display_colour.green
_definition.id '_display_colour.green'
loop_
_alias.definition_id
'_display_colour.green'
_name.category_id display_colour
_name.object_id green
_type.contents Index
_type.purpose Number
_description.text
;
Integer value between 0 and 255 giving the intensity of a
specific colour component (red, green or blue) for the RBG
display colour code.
;
_enumeration.range 0:255
_type.source Recorded
_type.container Single
_definition.update 2012-10-16
_units.code none
save_
save__display_colour.hue
_definition.id '_display_colour.hue'
loop_
_alias.definition_id
'_display_colour.hue'
_definition.update 2012-05-07
_description.text
;
Colour hue as an enumerated code.
;
_name.category_id display_colour
_name.object_id hue
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
_enumeration.default black
loop_
_enumeration_set.state
_enumeration_set.detail
black '[ 000, 000, 000 ]'
white '[ 255, 255, 255 ]'
grey '[ 192, 192, 192 ]'
grey_light '[ 211, 211, 211 ]'
grey_slate '[ 112, 128, 144 ]'
blue '[ 000, 000, 255 ]'
blue_light '[ 176, 224, 230 ]'
blue_medium '[ 000, 000, 205 ]'
blue_dark '[ 025, 025, 112 ]'
blue_navy '[ 000, 000, 128 ]'
blue_royal '[ 065, 105, 225 ]'
blue_sky '[ 135, 206, 235 ]'
blue_steel '[ 070, 130, 180 ]'
turquoise '[ 064, 224, 208 ]'
cyan '[ 000, 255, 255 ]'
cyan_light '[ 224, 255, 255 ]'
green '[ 000, 255, 000 ]'
green_light '[ 152, 251, 152 ]'
green_dark '[ 000, 100, 000 ]'
green_sea '[ 046, 139, 087 ]'
green_lime '[ 050, 205, 050 ]'
green_olive '[ 107, 142, 035 ]'
green_khaki '[ 240, 230, 140 ]'
yellow '[ 255, 255, 000 ]'
yellow_light '[ 255, 255, 224 ]'
yellow_gold '[ 255, 215, 000 ]'
brown '[ 165, 042, 042 ]'
brown_sienna '[ 160, 082, 045 ]'
brown_beige '[ 245, 245, 220 ]'
brown_tan '[ 210, 180, 140 ]'
salmon '[ 250, 128, 114 ]'
salmon_light '[ 255, 160, 122 ]'
salmon_dark '[ 233, 150, 122 ]'
orange '[ 255, 165, 000 ]'
orange_dark '[ 255, 140, 000 ]'
red '[ 255, 000, 000 ]'
red_coral '[ 255, 127, 080 ]'
red_tomato '[ 255, 099, 071 ]'
red_orange '[ 255, 069, 000 ]'
red_violet '[ 219, 112, 147 ]'
red_maroon '[ 176, 048, 096 ]'
pink '[ 255, 192, 203 ]'
pink_light '[ 255, 182, 193 ]'
pink_deep '[ 255, 020, 147 ]'
pink_hot '[ 255, 105, 180 ]'
violet '[ 238, 130, 238 ]'
violet_red '[ 208, 032, 144 ]'
violet_magenta '[ 255, 000, 255 ]'
violet_dark '[ 148, 000, 211 ]'
violet_blue '[ 138, 043, 226 ]'
save_
save__display_colour.key
_definition.id '_display_colour.key'
loop_
_alias.definition_id
'_display_colour.key'
_definition.update 2012-05-07
_description.text
;
Value is a unique key to a set of DISPLAY_COLOUR items
in a looped list.
;
_name.category_id display_colour
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _display_colour.key = _display_colour.hue'
save_
save__display_colour.red
_definition.id '_display_colour.red'
loop_
_alias.definition_id
'_display_colour.red'
_name.category_id display_colour
_name.object_id red
_type.contents Index
_type.purpose Number
_description.text
;
Integer value between 0 and 255 giving the intensity of a
specific colour component (red, green or blue) for the RBG
display colour code.
;
_enumeration.range 0:255
_type.source Recorded
_type.container Single
_definition.update 2012-10-16
_units.code none
save_
save__display_colour.RGB
_definition.id '_display_colour.RGB'
loop_
_alias.definition_id
'_display_colour.RGB'
_definition.update 2012-11-20
_description.text
;
The red-green-blue intensities, bases 256, for each colour code.
;
_name.category_id display_colour
_name.object_id RGB
_type.purpose Number
_type.source Derived
_type.container List
_type.contents Integer
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With c as display_colour
_display_colour.RGB = [ c.red, c.green, c.blue ]
;
save_
save_JOURNAL
_definition.id JOURNAL
_definition.scope Category
_definition.class Set
_definition.update 2012-12-11
_description.text
;
Category of items recording details about the book-keeping
by the journal staff when processing a CIF submitted for
publication. The creator of a CIF will not normally specify
these data items. The data names are not defined in the
dictionary because they are for journal use only.
;
_name.category_id PUBLICATION
_name.object_id JOURNAL
save_
save__journal.coden_ASTM
_definition.id '_journal.coden_ASTM'
loop_
_alias.definition_id
'_journal.coden_ASTM'
'_journal_coden_ASTM'
_definition.update 2012-12-11
_description.text
;
ASTM code assigned to journal.
;
_name.category_id journal
_name.object_id coden_ASTM
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__journal.coden_Cambridge
_definition.id '_journal.coden_Cambridge'
loop_
_alias.definition_id
'_journal.coden_Cambridge'
'_journal_coden_Cambridge'
_definition.update 2012-12-11
_description.text
;
Cambridge Cryst. Data Centre code assigned to journal.
;
_name.category_id journal
_name.object_id coden_Cambridge
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__journal.data_validation_number
_definition.id '_journal.data_validation_number'
loop_
_alias.definition_id
'_journal.data_validation_number'
'_journal_data_validation_number'
_definition.update 2014-06-12
_description.text
;
Journal data items are defined by the journal staff.
;
_name.category_id journal
_name.object_id 'data_validation_number'
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save__journal.issue
_definition.id '_journal.issue'
loop_
_alias.definition_id
'_journal.issue'
'_journal_issue'
_definition.update 2012-12-11
_description.text
;
Issue identifier within the journal.
;
_name.category_id journal
_name.object_id issue
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save__journal.language
_definition.id '_journal.language'
loop_
_alias.definition_id
'_journal.language'
'_journal_language'
_definition.update 2012-12-11
_description.text
;
Language of the publication.
;
_name.category_id journal
_name.object_id language
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__journal.name_full
_definition.id '_journal.name_full'
loop_
_alias.definition_id
'_journal.name_full'
'_journal_name_full'
_definition.update 2012-12-11
_description.text
;
Full name of the journal.
;
_name.category_id journal
_name.object_id name_full
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__journal.page_first
_definition.id '_journal.page_first'
loop_
_alias.definition_id
'_journal.page_first'
'_journal_page_first'
_definition.update 2012-12-11
_description.text
;
First page of the publication in the journal.
;
_name.category_id journal
_name.object_id page_first
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Integer
_enumeration.default 1
save_
save__journal.page_last
_definition.id '_journal.page_last'
loop_
_alias.definition_id
'_journal.page_last'
'_journal_page_last'
_definition.update 2012-12-11
_description.text
;
Last page of the publication in the journal.
;
_name.category_id journal
_name.object_id page_last
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Integer
_enumeration.range 1:
save_
save__journal.paper_category
_definition.id '_journal.paper_category'
loop_
_alias.definition_id
'_journal.paper_category'
'_journal_paper_category'
_definition.update 2012-12-11
_description.text
;
Category of the publication in the journal.
;
_name.category_id journal
_name.object_id paper_category
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save__journal.paper_doi
_definition.id '_journal.paper_doi'
loop_
_alias.definition_id
'_journal.paper_doi'
'_journal_paper_doi'
_definition.update 2012-12-11
_description.text
;
DOI of the publication in the journal.
;
_name.category_id journal
_name.object_id paper_doi
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save__journal.suppl_publ_number
_definition.id '_journal.suppl_publ_number'
loop_
_alias.definition_id
'_journal.suppl_publ_number'
'_journal_suppl_publ_number'
_definition.update 2012-12-11
_description.text
;
Number of supplementary publication.
;
_name.category_id journal
_name.object_id suppl_publ_number
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save__journal.suppl_publ_pages
_definition.id '_journal.suppl_publ_pages'
loop_
_alias.definition_id
'_journal.suppl_publ_pages'
'_journal_suppl_publ_pages'
_definition.update 2012-12-11
_description.text
;
Number of pages in the supplementary publication.
;
_name.category_id journal
_name.object_id suppl_publ_pages
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Integer
_enumeration.range 1:
save_
save__journal.validation_number
_definition.id '_journal.validation_number'
loop_
_alias.definition_id
'_journal.validation_number'
_definition.update 2013-01-23
_description.text
;
Data validation number assigned to journal.
;
_name.category_id journal
_name.object_id validation_number
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__journal.volume
_definition.id '_journal.volume'
loop_
_alias.definition_id
'_journal.volume'
'_journal_volume'
_definition.update 2012-12-11
_description.text
;
Volume number of the publication.
;
_name.category_id journal
_name.object_id volume
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Integer
_enumeration.range 1:
save_
save__journal.year
_definition.id '_journal.year'
loop_
_alias.definition_id
'_journal.year'
'_journal_year'
_definition.update 2012-12-11
_description.text
;
Year of the publication.
;
_name.category_id journal
_name.object_id year
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Integer
_enumeration.range 1700:2100
save_
save_JOURNAL_COEDITOR
_definition.id JOURNAL_COEDITOR
_definition.scope Category
_definition.class Set
_definition.update 2012-12-11
_description.text
;
Category of items recording co-editor details.
;
_name.category_id JOURNAL
_name.object_id JOURNAL_COEDITOR
save_
save__journal_coeditor.address
_definition.id '_journal_coeditor.address'
loop_
_alias.definition_id
'_journal_coeditor.address'
'_journal_coeditor_address'
'_journal.coeditor_address'
_definition.update 2012-12-11
_description.text
;
The postal address of the coeditor.
;
_name.category_id journal_coeditor
_name.object_id address
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__journal_coeditor.code
_definition.id '_journal_coeditor.code'
loop_
_alias.definition_id
'_journal_coeditor.code'
'_journal_coeditor_code'
'_journal.coeditor_code'
_definition.update 2012-12-11
_description.text
;
The coeditor identifier.
;
_name.category_id journal_coeditor
_name.object_id code
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save__journal_coeditor.email
_definition.id '_journal_coeditor.email'
loop_
_alias.definition_id
'_journal_coeditor.email'
'_journal_coeditor_email'
'_journal.coeditor_email'
_definition.update 2012-12-11
_description.text
;
The email address of the coeditor.
;
_name.category_id journal_coeditor
_name.object_id email
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__journal_coeditor.fax
_definition.id '_journal_coeditor.fax'
loop_
_alias.definition_id
'_journal_coeditor.fax'
'_journal_coeditor_fax'
'_journal.coeditor_fax'
_definition.update 2012-12-11
_description.text
;
The fax number of the coeditor.
;
_name.category_id journal_coeditor
_name.object_id fax
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents text
save_
save__journal_coeditor.name
_definition.id '_journal_coeditor.name'
loop_
_alias.definition_id
'_journal_coeditor.name'
'_journal_coeditor_name'
'_journal.coeditor_name'
_definition.update 2012-12-11
_description.text
;
The name of the coeditor.
;
_name.category_id journal_coeditor
_name.object_id name
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__journal_coeditor.notes
_definition.id '_journal_coeditor.notes'
loop_
_alias.definition_id
'_journal_coeditor.notes'
'_journal_coeditor_notes'
'_journal.coeditor_notes'
_definition.update 2012-12-11
_description.text
;
Notes on coeditor interaction wrt this publication.
;
_name.category_id journal_coeditor
_name.object_id notes
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__journal_coeditor.phone
_definition.id '_journal_coeditor.phone'
loop_
_alias.definition_id
'_journal_coeditor.phone'
'_journal_coeditor_phone'
'_journal.coeditor_phone'
_definition.update 2012-12-11
_description.text
;
The phone number of the coeditor.
;
_name.category_id journal_coeditor
_name.object_id phone
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents text
save_
save_JOURNAL_DATE
_definition.id JOURNAL_DATE
_definition.scope Category
_definition.class Set
_definition.update 2012-12-11
_description.text
;
Category of items recording dates of publication processing.
;
_name.category_id JOURNAL
_name.object_id JOURNAL_DATE
save_
save__journal_date.accepted
_definition.id '_journal_date.accepted'
loop_
_alias.definition_id
'_journal_date.accepted'
'_journal_date_accepted'
'_journal.date_accepted'
_definition.update 2012-12-11
_description.text
;
Date the publication was accepted.
;
_name.category_id journal_date
_name.object_id accepted
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Date
save_
save__journal_date.from_coeditor
_definition.id '_journal_date.from_coeditor'
loop_
_alias.definition_id
'_journal_date.from_coeditor'
'_journal_date_from_coeditor'
'_journal.date_from_coeditor'
_definition.update 2012-12-11
_description.text
;
Date the publication recieved from coeditor.
;
_name.category_id journal_date
_name.object_id from_coeditor
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Date
save_
save__journal_date.printers_final
_definition.id '_journal_date.printers_final'
loop_
_alias.definition_id
'_journal_date.printers_final'
'_journal_date_printers_final'
'_journal.date_printers_final'
_definition.update 2012-12-11
_description.text
;
Date the publication last sent to the printers.
;
_name.category_id journal_date
_name.object_id printers_final
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Date
save_
save__journal_date.printers_first
_definition.id '_journal_date.printers_first'
loop_
_alias.definition_id
'_journal_date.printers_first'
'_journal_date_printers_first'
'_journal.date_printers_first'
_definition.update 2012-12-11
_description.text
;
Date the publication first sent to the printers.
;
_name.category_id journal_date
_name.object_id printers_first
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Date
save_
save__journal_date.proofs_in
_definition.id '_journal_date.proofs_in'
loop_
_alias.definition_id
'_journal_date.proofs_in'
'_journal_date_proofs_in'
'_journal.date_proofs_in'
_definition.update 2012-12-11
_description.text
;
Date the publication proofs recieved.
;
_name.category_id journal_date
_name.object_id proofs_in
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Date
save_
save__journal_date.proofs_out
_definition.id '_journal_date.proofs_out'
loop_
_alias.definition_id
'_journal_date.proofs_out'
'_journal_date_proofs_out'
'_journal.date_proofs_out'
_definition.update 2012-12-11
_description.text
;
Date the publication proofs sent out.
;
_name.category_id journal_date
_name.object_id proofs_out
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Date
save_
save__journal_date.recd_copyright
_definition.id '_journal_date.recd_copyright'
loop_
_alias.definition_id
'_journal_date.recd_copyright'
'_journal_date_recd_copyright'
'_journal.date_recd_copyright'
_definition.update 2012-12-11
_description.text
;
Date completed copyright recieved.
;
_name.category_id journal_date
_name.object_id recd_copyright
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Date
save_
save__journal_date.recd_electronic
_definition.id '_journal_date.recd_electronic'
loop_
_alias.definition_id
'_journal_date.recd_electronic'
'_journal_date_recd_electronic'
'_journal.date_recd_electronic'
_definition.update 2012-12-11
_description.text
;
Date publication recieved electronically.
;
_name.category_id journal_date
_name.object_id recd_electronic
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Date
save_
save__journal_date.recd_hard_copy
_definition.id '_journal_date.recd_hard_copy'
loop_
_alias.definition_id
'_journal_date.recd_hard_copy'
'_journal_date_recd_hard_copy'
'_journal.date_recd_hard_copy'
_definition.update 2012-12-11
_description.text
;
Date publication recieved as hard copy.
;
_name.category_id journal_date
_name.object_id recd_hard_copy
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Date
save_
save__journal_date.to_coeditor
_definition.id '_journal_date.to_coeditor'
loop_
_alias.definition_id
'_journal_date.to_coeditor'
'_journal_date_to_coeditor'
'_journal.date_to_coeditor'
_definition.update 2012-12-11
_description.text
;
Date the publication sent to the coeditor.
;
_name.category_id journal_date
_name.object_id to_coeditor
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Date
save_
save_JOURNAL_INDEX
_definition.id JOURNAL_INDEX
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
Category of items describing publication indices.
;
_name.category_id JOURNAL
_name.object_id JOURNAL_INDEX
_category.key_id '_journal_index.key'
_category.key_list ['_journal_index.id']
save_
save__journal_index.id
_definition.id '_journal_index.id'
loop_
_alias.definition_id
'_journal_index.id'
'_journal_index_id'
_definition.update 2013-01-23
_description.text
;
Index number identifier of the JOURNAL_INDEX category.
;
_name.category_id journal_index
_name.object_id id
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Index
_enumeration.range 1:
save_
save__journal_index.key
_definition.id '_journal_index.key'
loop_
_alias.definition_id
'_journal_index.key'
_definition.update 2012-12-13
_description.text
;
Value is a unique key to a set of JOURNAL_INDEX items
in a looped list.
;
_name.category_id journal_index
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Index
loop_
_method.purpose
_method.expression
Evaluation ' _journal_index.key = _journal_index.id'
save_
save__journal_index.subterm
_definition.id '_journal_index.subterm'
loop_
_alias.definition_id
'_journal_index.subterm'
'_journal_index_subterm'
_definition.update 2012-12-11
_description.text
;
Sub-term index assigned for the publication.
;
_name.category_id journal_index
_name.object_id subterm
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Text
save_
save__journal_index.term
_definition.id '_journal_index.term'
loop_
_alias.definition_id
'_journal_index.term'
'_journal_index_term'
_definition.update 2012-12-11
_description.text
;
Term index assigned for the publication.
;
_name.category_id journal_index
_name.object_id term
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Text
save_
save__journal_index.type
_definition.id '_journal_index.type'
loop_
_alias.definition_id
'_journal_index.type'
'_journal_index_type'
_definition.update 2012-12-11
_description.text
;
Type of index assigned for the publication.
;
_name.category_id journal_index
_name.object_id type
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
O '???????? formula ??????????????'
S '???????? structure description ???????'
_enumeration.default O
save_
save_JOURNAL_TECHEDITOR
_definition.id JOURNAL_TECHEDITOR
_definition.scope Category
_definition.class Set
_definition.update 2012-12-11
_description.text
;
Category of items recording details of the technical editor
processing this publication.
;
_name.category_id JOURNAL
_name.object_id JOURNAL_TECHEDITOR
save_
save__journal_techeditor.address
_definition.id '_journal_techeditor.address'
loop_
_alias.definition_id
'_journal_techeditor.address'
'_journal_techeditor_address'
'_journal.techeditor_address'
_definition.update 2012-12-11
_description.text
;
Postal address of the technical editor for this publication.
;
_name.category_id journal_techeditor
_name.object_id address
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__journal_techeditor.code
_definition.id '_journal_techeditor.code'
loop_
_alias.definition_id
'_journal_techeditor.code'
'_journal_techeditor_code'
'_journal.techeditor_code'
_definition.update 2012-12-11
_description.text
;
Code of the technical editor for this publication.
;
_name.category_id journal_techeditor
_name.object_id code
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save__journal_techeditor.email
_definition.id '_journal_techeditor.email'
loop_
_alias.definition_id
'_journal_techeditor.email'
'_journal_techeditor_email'
'_journal.techeditor_email'
_definition.update 2012-12-11
_description.text
;
Email address of the technical editor for this publication.
;
_name.category_id journal_techeditor
_name.object_id email
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__journal_techeditor.fax
_definition.id '_journal_techeditor.fax'
loop_
_alias.definition_id
'_journal_techeditor.fax'
'_journal_techeditor_fax'
'_journal.techeditor_fax'
_definition.update 2012-12-11
_description.text
;
Fax number of the technical editor for this publication.
;
_name.category_id journal_techeditor
_name.object_id fax
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__journal_techeditor.name
_definition.id '_journal_techeditor.name'
loop_
_alias.definition_id
'_journal_techeditor.name'
'_journal_techeditor_name'
'_journal.techeditor_name'
_definition.update 2012-12-11
_description.text
;
Name of the technical editor for this publication.
;
_name.category_id journal_techeditor
_name.object_id name
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__journal_techeditor.notes
_definition.id '_journal_techeditor.notes'
loop_
_alias.definition_id
'_journal_techeditor.notes'
'_journal_techeditor_notes'
'_journal.techeditor_notes'
_definition.update 2012-12-11
_description.text
;
Notes of the technical editor for this publication.
;
_name.category_id journal_techeditor
_name.object_id notes
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__journal_techeditor.phone
_definition.id '_journal_techeditor.phone'
loop_
_alias.definition_id
'_journal_techeditor.phone'
'_journal_techeditor_phone'
'_journal.techeditor_phone'
_definition.update 2012-12-11
_description.text
;
Phone number of the technical editor for this publication.
;
_name.category_id journal_techeditor
_name.object_id phone
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_PUBL
_definition.id PUBL
_definition.scope Category
_definition.class Set
_definition.update 2012-05-07
_description.text
;
Data items in the PUBL category are used when submitting a
manuscript for publication. They refer either to the paper as
a whole, or to specific named elements within a paper (such as
the title and abstract, or the Comment and Experimental
sections of Acta Crystallographica Section C). The data items
in the PUBL_BODY category should be used for the textual
content of other submissions. Typically, each journal will
supply a list of the specific items it requires in its Notes
for Authors.
;
_name.category_id PUBLICATION
_name.object_id PUBL
save_
save__publ.contact_letter
_definition.id '_publ.contact_letter'
loop_
_alias.definition_id
'_publ.contact_letter'
'_publ_contact_letter'
_definition.update 2012-11-29
_description.text
;
A letter submitted to the journal editor by the contact author.
;
_name.category_id publ
_name.object_id contact_letter
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_PUBL_AUTHOR
_definition.id PUBL_AUTHOR
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
Category of data items recording the author information.
;
_name.category_id PUBL
_name.object_id PUBL_AUTHOR
_category.key_id '_publ_author.key'
_category.key_list ['_publ_author.name']
save_
save__publ_author.address
_definition.id '_publ_author.address'
loop_
_alias.definition_id
'_publ_author.address'
'_publ_author_address'
_definition.update 2012-12-13
_description.text
;
The address of a publication author. If there is more than one
author, this will be looped with _publ_author_name.
;
_name.category_id publ_author
_name.object_id address
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
; Department
Institute
Street
City and postcode
COUNTRY
;
save_
save__publ_author.email
_definition.id '_publ_author.email'
loop_
_alias.definition_id
'_publ_author.email'
'_publ_author_email'
_definition.update 2012-12-13
_description.text
;
The e-mail address of a publication author. If there is more
than one author, this will be looped with _publ_author_name.
The format of e-mail addresses is given in Section 3.4, Address
Specification, of Internet Message Format, RFC 2822, P. Resnick
(Editor), Network Standards Group, April 2001.
;
_name.category_id publ_author
_name.object_id email
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_author.footnote
_definition.id '_publ_author.footnote'
loop_
_alias.definition_id
'_publ_author.footnote'
'_publ_author_footnote'
_definition.update 2012-12-13
_description.text
;
A footnote accompanying an author's name in the list of authors
of a paper. Typically indicates sabbatical address, additional
affiliations or date of decease.
;
_name.category_id publ_author
_name.object_id footnote
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_author.id_iucr
_definition.id '_publ_author.id_iucr'
loop_
_alias.definition_id
'_publ_author.id_iucr'
'_publ_author_id_iucr'
_definition.update 2012-12-13
_description.text
;
Identifier in the IUCr contact database of a publication
author. This identifier may be available from the World
Directory of Crystallographers (http://wdc.iucr.org).
;
_name.category_id publ_author
_name.object_id id_iucr
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Code
save_
save__publ_author.key
_definition.id '_publ_author.key'
loop_
_alias.definition_id
'_publ_author.key'
_definition.update 2012-12-13
_description.text
;
Value is a unique key to a set of PUBL_AUTHOR items
in a looped list.
;
_name.category_id publ_author
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Text
loop_
_method.purpose
_method.expression
Evaluation ' _publ_author.key = _publ_author.name'
save_
save__publ_author.name
_definition.id '_publ_author.name'
loop_
_alias.definition_id
'_publ_author.name'
'_publ_author_name'
_definition.update 2012-12-13
_description.text
;
The name of a publication author. If there are multiple authors,
this will be looped with _publ_author.address. The family
name(s), followed by a comma and including any dynastic
components, precedes the first names or initials.
;
_name.category_id publ_author
_name.object_id name
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A'
'M\"uller, H.A.'
'Ross II, C.R.'
save_
save__publ_author.phone
_definition.id '_publ_author.phone'
loop_
_alias.definition_id
'_publ_author.phone'
'_publ_author_phone'
_definition.update 2014-06-12
_description.text
;
Telephone number of the author submitting the manuscript and
data block.
The recommended style starts with the international dialing
prefix, followed by the area code in parentheses, followed by the
local number and any extension number prefixed by 'x',
with no spaces. The earlier convention of including
the international dialing prefix in parentheses is no longer
recommended.
;
_name.category_id publ_author
_name.object_id phone
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
12(34)9477330
12()349477330
12(34)9477330x5543
save_
save_PUBL_BODY
_definition.id PUBL_BODY
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
Data items in the PUBL_BODY category permit labelling of
different text sections within the body of a submitted paper.
Note that these should not be used in a paper which has
a standard format with sections tagged by specific data names
(such as in Acta Crystallographica Section C). Typically,
each journal will supply a list of the specific items it
requires in its Notes for Authors.
;
_name.category_id PUBL
_name.object_id PUBL_BODY
_category.key_id '_publ_body.key'
_category.key_list ['_publ_body.label']
save_
save__publ_body.contents
_definition.id '_publ_body.contents'
loop_
_alias.definition_id
'_publ_body.contents'
'_publ_body_contents'
_definition.update 2012-12-13
_description.text
;
A text section of a submitted paper.
;
_name.category_id publ_body
_name.object_id contents
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_body.element
_definition.id '_publ_body.element'
loop_
_alias.definition_id
'_publ_body.element'
'_publ_body_element'
_definition.update 2012-12-13
_description.text
;
The functional role of the associated text section.
;
_name.category_id publ_body
_name.object_id element
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
section
subsection
subsubsection
appendix
footnote
_enumeration.default section
save_
save__publ_body.format
_definition.id '_publ_body.format'
loop_
_alias.definition_id
'_publ_body.format'
'_publ_body_format'
_definition.update 2012-12-13
_description.text
;
Enumerated state indicating the appropriate typesetting
conventions for accented characters and special symbols
in the text section.
;
_name.category_id publ_body
_name.object_id format
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
ascii 'no coding for special symbols'
cif 'CIF convention'
latex LaTeX
rtf 'Rich Text Format'
sgml 'SGML (ISO 8879)'
tex TeX
troff 'troff or nroff'
_enumeration.default cif
save_
save__publ_body.key
_definition.id '_publ_body.key'
loop_
_alias.definition_id
'_publ_body.key'
_definition.update 2012-12-13
_description.text
;
Value is a unique key to a set of PUBL_BODY items
in a looped list.
;
_name.category_id publ_body
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _publ_body.key = _publ_body.label'
save_
save__publ_body.label
_definition.id '_publ_body.label'
loop_
_alias.definition_id
'_publ_body.label'
'_publ_body_label'
_definition.update 2012-12-13
_description.text
;
Unigue identifier for each part of the body of the paper.
;
_name.category_id publ_body
_name.object_id label
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_description_example.case
1
1.1
2.1.3
save_
save__publ_body.title
_definition.id '_publ_body.title'
loop_
_alias.definition_id
'_publ_body.title'
'_publ_body_title'
_definition.update 2012-12-13
_description.text
;
Title of the associated section of text.
;
_name.category_id publ_body
_name.object_id title
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_PUBL_CONTACT_AUTHOR
_definition.id PUBL_CONTACT_AUTHOR
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
Category of items describing contact author(s) details.
;
_name.category_id PUBL
_name.object_id PUBL_CONTACT_AUTHOR
_category.key_id '_publ_contact_author.key'
_category.key_list ['_publ_contact_author.name']
save_
save__publ_contact_author.address
_definition.id '_publ_contact_author.address'
loop_
_alias.definition_id
'_publ_contact_author.address'
'_publ_contact_author_address'
'_publ.contact_author_address'
_definition.update 2012-11-29
_description.text
;
The address of the author submitting the manuscript and
data block. This is the person contacted by the journal
editorial staff.
;
_name.category_id publ_contact_author
_name.object_id address
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
; Department of Chemistry and Biochemistry
University of Guelph
Ontario
Canada
N1G 2W1
;
save_
save__publ_contact_author.email
_definition.id '_publ_contact_author.email'
loop_
_alias.definition_id
'_publ_contact_author.email'
'_publ_contact_author_email'
'_publ.contact_author_email'
_definition.update 2014-06-12
_description.text
;
E-mail address in a form recognizable to international networks.
The format of e-mail addresses is given in Section 3.4, Address
Specification, of Internet Message Format, RFC 2822, P. Resnick
(Editor), Network Standards Group, April 2001.
;
_name.category_id publ_contact_author
_name.object_id email
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
name@host.domain.country
banjo.patterson@gulgong.edu.au
save_
save__publ_contact_author.fax
_definition.id '_publ_contact_author.fax'
loop_
_alias.definition_id
'_publ_contact_author.fax'
'_publ_contact_author_fax'
'_publ.contact_author_fax'
_definition.update 2012-11-29
_description.text
;
Facsimile telephone number of the author submitting the manuscript
and data block.
The recommended style is the international dialing prefix, followed
by the area code in parentheses, followed by the local number with
no spaces. The earlier convention of including the international
dialing prefix in parentheses is no longer recommended.
;
_name.category_id publ_contact_author
_name.object_id fax
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_contact_author.id_iucr
_definition.id '_publ_contact_author.id_iucr'
loop_
_alias.definition_id
'_publ_contact_author.id_iucr'
'_publ_contact_author_id_iucr'
_definition.update 2012-11-29
_description.text
;
Identifier in the IUCr contact database of the author submitting
the manuscript and datablock. This identifier may be available
from the World Directory of Crystallographers (http://wdc.iucr.org).
;
_name.category_id publ_contact_author
_name.object_id id_iucr
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_contact_author.key
_definition.id '_publ_contact_author.key'
loop_
_alias.definition_id
'_publ_contact_author.key'
_definition.update 2012-12-13
_description.text
;
Value is a unique key to a set of PUBL_CONTACT_AUTHOR items
in a looped list.
;
_name.category_id publ_contact_author
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Text
loop_
_method.purpose
_method.expression
Evaluation ' _publ_contact_author.key = _publ_contact_author.name'
save_
save__publ_contact_author.name
_definition.id '_publ_contact_author.name'
loop_
_alias.definition_id
'_publ_contact_author.name'
'_publ_contact_author_name'
'_publ.contact_author'
'_publ_contact_author'
'_publ.contact_author_name'
_definition.update 2012-11-29
_description.text
;
The name of the author(s) submitting the manuscript and
data block. This is the person contacted by the journal
editorial staff.
;
_name.category_id publ_contact_author
_name.object_id name
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'Professor George Ferguson'
save_
save__publ_contact_author.phone
_definition.id '_publ_contact_author.phone'
loop_
_alias.definition_id
'_publ_contact_author.phone'
'_publ_contact_author_phone'
'_publ.contact_author_phone'
_definition.update 2012-11-29
_description.text
;
Telephone number of author submitting the manuscript and data block.
The recommended style is the international dialing prefix,
followed by the area code in parentheses, followed by the
local number and any extension number prefixed by 'x', with
no spaces. The earlier convention of including the international
dialing prefix in parentheses is no longer recommended.
;
_name.category_id publ_contact_author
_name.object_id phone
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
12(34)9477330
12()349477330
12(34)9477330x5543
save_
save_PUBL_MANUSCRIPT
_definition.id PUBL_MANUSCRIPT
_definition.scope Category
_definition.class Set
_definition.update 2012-12-13
_description.text
;
Category of items describing the publication manuscript.
;
_name.category_id PUBL
_name.object_id PUBL_MANUSCRIPT
save_
save__publ_manuscript.creation
_definition.id '_publ_manuscript.creation'
loop_
_alias.definition_id
'_publ_manuscript.creation'
'_publ_manuscript_creation'
'_publ.manuscript_creation'
_definition.update 2012-11-29
_description.text
;
A description of the wordprocessor package and computer used to
create the manuscript stored as publ_manuscript.processed.
;
_name.category_id publ_manuscript
_name.object_id creation
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_manuscript.processed
_definition.id '_publ_manuscript.processed'
loop_
_alias.definition_id
'_publ_manuscript.processed'
'_publ_manuscript_processed'
'_publ.manuscript_processed'
_definition.update 2012-11-29
_description.text
;
The full manuscript of a paper (excluding possibly the figures
and the tables) output in ASCII characters from a word processor.
Information about the generation of this data item must be
specified in the data item _publ_manuscript.creation.
;
_name.category_id publ_manuscript
_name.object_id processed
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_manuscript.text
_definition.id '_publ_manuscript.text'
loop_
_alias.definition_id
'_publ_manuscript.text'
'_publ_manuscript_text'
'_publ.manuscript_text'
_definition.update 2012-11-29
_description.text
;
The full manuscript of a paper (excluding figures and possibly
the tables) output as standard ASCII text.
;
_name.category_id publ_manuscript
_name.object_id text
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_PUBL_MANUSCRIPT_INCL_EXTRA
_definition.id PUBL_MANUSCRIPT_INCL_EXTRA
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
Category of data items that allow the authors of a manuscript to
submit for publication data names that should be added to the
standard request list employed by journal printing software.
Although these fields are primarily intended to identify CIF data
items that the author wishes to include in a published paper, they
can also be used to identify data names created so that non-CIF items
can be included in the publication. Note that *.item names MUST be
enclosed in single quotes.
;
_name.category_id PUBL_MANUSCRIPT
_name.object_id PUBL_MANUSCRIPT_INCL_EXTRA
_category.key_id '_publ_manuscript_incl_extra.key'
_category.key_list ['_publ_manuscript_incl_extra.item']
save_
save__publ_manuscript_incl_extra.defn
_definition.id '_publ_manuscript_incl_extra.defn'
loop_
_alias.definition_id
'_publ_manuscript_incl_extra.defn'
'_publ_manuscript_incl_extra_defn'
'_publ_manuscript_incl.extra_defn'
_definition.update 2012-12-13
_description.text
;
Yes/No flags whether the corresponding data item marked for inclusion
in a journal request list is a standard CIF definition or not.
;
_name.category_id publ_manuscript_incl_extra
_name.object_id defn
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
yes 'include item in journal request list'
y 'include item in journal request list'
no 'exclude item in journal request list'
n 'exclude item in journal request list'
_enumeration.default yes
save_
save__publ_manuscript_incl_extra.info
_definition.id '_publ_manuscript_incl_extra.info'
loop_
_alias.definition_id
'_publ_manuscript_incl_extra.info'
'_publ_manuscript_incl_extra_info'
'_publ_manuscript_incl.extra_info'
_definition.update 2012-12-13
_description.text
;
A short note indicating the reason why the author wishes the
corresponding data item marked for inclusion in the journal
request list to be published.
;
_name.category_id publ_manuscript_incl_extra
_name.object_id info
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_manuscript_incl_extra.item
_definition.id '_publ_manuscript_incl_extra.item'
loop_
_alias.definition_id
'_publ_manuscript_incl_extra.item'
'_publ_manuscript_incl_extra_item'
'_publ_manuscript_incl.extra_item'
_definition.update 2012-12-13
_description.text
;
The data name (i.e. Tag) of a specific data item included in the
manuscript which is not normally requested by the journal. The values
of this item are the extra data names (which MUST be enclosed
in single quotes) that will be added to the journal request list.
;
_name.category_id publ_manuscript_incl_extra
_name.object_id item
_type.purpose Link
_type.source Assigned
_type.container Single
_type.contents Tag
save_
save__publ_manuscript_incl_extra.key
_definition.id '_publ_manuscript_incl_extra.key'
loop_
_alias.definition_id
'_publ_manuscript_incl_extra.key'
_definition.update 2012-12-13
_description.text
;
Value is a unique key to a set of PUBL_MANUSCRIPT_INCL_EXTRA items
in a looped list.
;
_name.category_id publ_manuscript_incl_extra
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Tag
loop_
_method.purpose
_method.expression
Evaluation ' _publ_manuscript_incl_extra.key = _publ_manuscript_incl_extra.item'
save_
save_PUBL_REQUESTED
_definition.id PUBL_REQUESTED
_definition.scope Category
_definition.class Set
_definition.update 2012-12-13
_description.text
;
CATEGORY of data items that enable the author to make
specific requests to the journal office for processing.
;
_name.category_id PUBL
_name.object_id PUBL_REQUESTED
save_
save__publ_requested.category
_definition.id '_publ_requested.category'
loop_
_alias.definition_id
'_publ_requested.category'
'_publ_requested_category'
'_publ.requested_category'
_definition.update 2012-12-13
_description.text
;
The category of paper submitted. For submission to Acta
Crystallographica Section C or Acta Crystallographica
Section E, ONLY those codes indicated for use with those
journals should be used.
;
_name.category_id publ_requested
_name.object_id category
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
FA 'Full article'
FI 'Full submission - inorganic (Acta C)'
FO 'Full submission - organic (Acta C)'
FM 'Full submission - metal-organic (Acta C)'
CI 'CIF-access paper - inorganic (Acta C)'
CO 'CIF-access paper - organic (Acta C)'
CM 'CIF-access paper - metal-organic (Acta C)'
EI 'Electronic submission - inorganic (Acta E)'
EO 'Electronic submission - organic (Acta E)'
EM 'Electronic submission - metal-organic (Acta E)'
AD 'Addenda & Errata (Acta C, Acta E)'
SC 'Short Communication'
_enumeration.default FA
save_
save__publ_requested.coeditor_name
_definition.id '_publ_requested.coeditor_name'
loop_
_alias.definition_id
'_publ_requested.coeditor_name'
'_publ_requested_coeditor_name'
'_publ.requested_coeditor_name'
_definition.update 2012-12-13
_description.text
;
The name of the Co-editor whom the authors would like to
process the submitted manuscript.
;
_name.category_id publ_requested
_name.object_id coeditor_name
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_requested.journal
_definition.id '_publ_requested.journal'
loop_
_alias.definition_id
'_publ_requested.journal'
'_publ_requested_journal'
'_publ.requested_journal'
_definition.update 2012-12-13
_description.text
;
Name of the journal to which the manuscript is being submitted.
;
_name.category_id publ_requested
_name.object_id journal
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_PUBL_SECTION
_definition.id PUBL_SECTION
_definition.scope Category
_definition.class Set
_definition.update 2012-05-07
_description.text
;
Manuscript section data if submitted in parts. see also
_publ_manuscript.text and _publ_manuscript.processed.
The _publ_section.exptl_prep, _publ_section.exptl_refinement
and _publ_section.exptl_solution items are preferred for
separating the chemical preparation, refinement and structure
solution aspects of the experimental description.
;
_name.category_id PUBL
_name.object_id PUBL_SECTION
save_
save__publ_section.abstract
_definition.id '_publ_section.abstract'
loop_
_alias.definition_id
'_publ_section.abstract'
'_publ_section_abstract'
'_publ.section_abstract'
_definition.update 2012-11-29
_description.text
;
The abstract of the submitted paper.
;
_name.category_id publ_section
_name.object_id abstract
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_section.acknowledgements
_definition.id '_publ_section.acknowledgements'
loop_
_alias.definition_id
'_publ_section.acknowledgements'
'_publ_section_acknowledgements'
'_publ.section_acknowledgements'
_definition.update 2012-11-29
_description.text
;
The acknowledgements section of the submitted paper.
;
_name.category_id publ_section
_name.object_id acknowledgements
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_section.comment
_definition.id '_publ_section.comment'
loop_
_alias.definition_id
'_publ_section.comment'
'_publ_section_comment'
'_publ.section_comment'
_definition.update 2013-02-22
_description.text
;
The comment section of the submitted paper.
;
_name.category_id publ_section
_name.object_id comment
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_section.discussion
_definition.id '_publ_section.discussion'
loop_
_alias.definition_id
'_publ_section.discussion'
'_publ_section_discussion'
'_publ.section_discussion'
_definition.update 2012-11-29
_description.text
;
The discussion section of the submitted paper.
;
_name.category_id publ_section
_name.object_id discussion
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_section.experimental
_definition.id '_publ_section.experimental'
loop_
_alias.definition_id
'_publ_section.experimental'
'_publ_section_experimental'
'_publ.section_experimental'
_definition.update 2012-11-29
_description.text
;
The experimental section of the submitted paper.
;
_name.category_id publ_section
_name.object_id experimental
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_section.exptl_prep
_definition.id '_publ_section.exptl_prep'
loop_
_alias.definition_id
'_publ_section.exptl_prep'
'_publ_section_exptl_prep'
'_publ.section_exptl_prep'
_definition.update 2012-11-29
_description.text
;
The experimental preparation section of the submitted paper.
;
_name.category_id publ_section
_name.object_id exptl_prep
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_section.exptl_refinement
_definition.id '_publ_section.exptl_refinement'
loop_
_alias.definition_id
'_publ_section.exptl_refinement'
'_publ_section_exptl_refinement'
'_publ.section_exptl_refinement'
_definition.update 2012-11-29
_description.text
;
The experimental refinement section of the submitted paper.
;
_name.category_id publ_section
_name.object_id exptl_refinement
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_section.exptl_solution
_definition.id '_publ_section.exptl_solution'
loop_
_alias.definition_id
'_publ_section.exptl_solution'
'_publ_section_exptl_solution'
'_publ.section_exptl_solution'
_definition.update 2012-11-29
_description.text
;
The experimental solution section of the submitted paper.
;
_name.category_id publ_section
_name.object_id exptl_solution
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_section.figure_captions
_definition.id '_publ_section.figure_captions'
loop_
_alias.definition_id
'_publ_section.figure_captions'
'_publ_section_figure_captions'
'_publ.section_figure_captions'
_definition.update 2012-11-29
_description.text
;
The figure captions of the submitted paper.
;
_name.category_id publ_section
_name.object_id figure_captions
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_section.introduction
_definition.id '_publ_section.introduction'
loop_
_alias.definition_id
'_publ_section.introduction'
'_publ_section_introduction'
'_publ.section_introduction'
_definition.update 2012-11-29
_description.text
;
The introduction section of the submitted paper.
;
_name.category_id publ_section
_name.object_id introduction
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_section.keywords
_definition.id '_publ_section.keywords'
loop_
_alias.definition_id
'_publ_section.keywords'
'_publ_section_keywords'
'_publ.section_keywords'
_definition.update 2012-11-29
_description.text
;
The keywords of the submitted paper.
;
_name.category_id publ_section
_name.object_id keywords
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_section.references
_definition.id '_publ_section.references'
loop_
_alias.definition_id
'_publ_section.references'
'_publ_section_references'
'_publ.section_references'
_definition.update 2012-11-29
_description.text
;
The references section of the submitted paper.
;
_name.category_id publ_section
_name.object_id references
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_section.related_literature
_definition.id '_publ_section.related_literature'
loop_
_alias.definition_id
'_publ_section.related_literature'
'_publ_section_related_literature'
'_publ.section_related_literature'
_definition.update 2012-11-29
_description.text
;
The related literature section of the submitted paper.
;
_name.category_id publ_section
_name.object_id related_literature
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_section.synopsis
_definition.id '_publ_section.synopsis'
loop_
_alias.definition_id
'_publ_section.synopsis'
'_publ_section_synopsis'
'_publ.section_synopsis'
_definition.update 2012-11-29
_description.text
;
The synopsis of the submitted paper.
;
_name.category_id publ_section
_name.object_id synopsis
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_section.table_legends
_definition.id '_publ_section.table_legends'
loop_
_alias.definition_id
'_publ_section.table_legends'
'_publ_section_table_legends'
'_publ.section_table_legends'
_definition.update 2012-11-29
_description.text
;
The table legends of the submitted paper.
;
_name.category_id publ_section
_name.object_id table_legends
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_section.title
_definition.id '_publ_section.title'
loop_
_alias.definition_id
'_publ_section.title'
'_publ_section_title'
'_publ.section_title'
_definition.update 2012-11-29
_description.text
;
The full title of the submitted paper.
;
_name.category_id publ_section
_name.object_id title
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__publ_section.title_footnote
_definition.id '_publ_section.title_footnote'
loop_
_alias.definition_id
'_publ_section.title_footnote'
'_publ_section_title_footnote'
'_publ.section_title_footnote'
_definition.update 2012-11-29
_description.text
;
Footnote (if any) to the title of the submitted paper.
;
_name.category_id publ_section
_name.object_id title_footnote
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_STRUCTURE
_definition.id STRUCTURE
_definition.scope Category
_definition.class Set
_definition.update 2012-11-20
_description.text
;
The DICTIONARY group encompassing the CORE STRUCTURE data items defined
and used with in the Crystallographic Information Framework (CIF).
;
_name.category_id CIF_CORE
_name.object_id STRUCTURE
save_
save_ATOM
_definition.id ATOM
_definition.scope Category
_definition.class Set
_definition.update 2012-11-20
_description.text
;
The CATEGORY of data items used to describe atomic information
used in crystallographic structure studies.
;
_name.category_id STRUCTURE
_name.object_id ATOM
save_
save_ATOM_SITE
_definition.id ATOM_SITE
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to describe atom site information
used in crystallographic structure studies.
;
_name.category_id ATOM
_name.object_id ATOM_SITE
_category.key_id '_atom_site.key'
_category.key_list ['_atom_site.label']
save_
save__atom_site.adp_type
_definition.id '_atom_site.adp_type'
loop_
_alias.definition_id
'_atom_site.adp_type'
'_atom_site_adp_type'
'_atom_site_thermal_displace_type'
'_atom_site.thermal_displace_type'
_definition.update 2012-11-20
_description.text
;
Code for type of atomic displacement parameters used for the site.
;
_name.category_id atom_site
_name.object_id adp_type
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
Uani 'anisotropic Uij'
Uiso 'isotropic U'
Uovl 'overall U'
Umpe 'multipole expansion U'
Bani 'anisotropic Bij'
Biso 'isotropic B'
Bovl 'overall B'
_enumeration.default Uiso
save_
save__atom_site.attached_hydrogens
_definition.id '_atom_site.attached_hydrogens'
loop_
_alias.definition_id
'_atom_site.attached_hydrogens'
'_atom_site_attached_hydrogens'
_definition.update 2012-11-20
_description.text
;
Number of hydrogen atoms attached to the atom at this site
excluding any H atoms for which coordinates (measured or calculated)
are given.
;
_name.category_id atom_site
_name.object_id attached_hydrogens
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 0:8
_enumeration.default 0
loop_
_description_example.case
_description_example.detail
2 'water oxygen'
1 'hydroxyl oxygen'
4 'ammonium nitrogen'
save_
save__atom_site.B_equiv_geom_mean
_definition.id '_atom_site.B_equiv_geom_mean'
loop_
_alias.definition_id
'_atom_site.B_equiv_geom_mean'
'_atom_site_B_equiv_geom_mean'
_definition.update 2012-11-20
_description.text
;
Equivalent isotropic atomic displacement parameter, B(equiv),
in angstroms squared, calculated as the geometric mean of
the anisotropic atomic displacement parameters.
B(equiv) = (B~i~ B~j~ B~k~)^1/3^
B~n~ = the principal components of the orthogonalised B^ij^
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_name.category_id atom_site
_name.object_id B_equiv_geom_mean
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstrom_squared
save_
save__atom_site.B_equiv_geom_mean_su
_definition.id '_atom_site.B_equiv_geom_mean_su'
loop_
_alias.definition_id
'_atom_site.B_equiv_geom_mean_su'
'_atom_site_B_equiv_geom_mean_su'
'_atom_site.B_equiv_geom_mean_esd'
_definition.update 2012-11-20
_description.text
;
Standard Uncertainty value for the
Equivalent isotropic atomic displacement parameter, B(equiv),
in angstroms squared, calculated as the geometric mean of
the anisotropic atomic displacement parameters.
;
_name.category_id atom_site
_name.object_id B_equiv_geom_mean_su
_name.linked_item_id '_atom_site.B_equiv_geom_mean'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstrom_squared
save_
save__atom_site.B_iso_or_equiv
_definition.id '_atom_site.B_iso_or_equiv'
loop_
_alias.definition_id
'_atom_site.B_iso_or_equiv'
'_atom_site_B_iso_or_equiv'
_definition.update 2012-11-20
_description.text
;
Isotropic atomic displacement parameter, or equivalent isotropic
atomic displacement parameter, B(equiv), in angstroms squared,
calculated from anisotropic temperature factor parameters.
B(equiv) = (1/3) sum~i~[sum~j~(B^ij^ a*~i~ a*~j~ a~i~ a~j~)]
a = the real-space cell lengths
a* = the reciprocal-space cell lengths
B^ij^ = 8 pi^2^ U^ij^
Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_name.category_id atom_site
_name.object_id B_iso_or_equiv
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstrom_squared
save_
save__atom_site.B_iso_or_equiv_su
_definition.id '_atom_site.B_iso_or_equiv_su'
loop_
_alias.definition_id
'_atom_site.B_iso_or_equiv_su'
'_atom_site_B_iso_or_equiv_su'
'_atom_site.B_iso_or_equiv_esd'
_definition.update 2012-11-20
_description.text
;
Standard Uncertainty value for the
Isotropic atomic displacement parameter, or equivalent isotropic
atomic displacement parameter, B(equiv), in angstroms squared,
calculated from anisotropic temperature factor parameters.
;
_name.category_id atom_site
_name.object_id B_iso_or_equiv_su
_name.linked_item_id '_atom_site.B_iso_or_equiv'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstrom_squared
save_
save__atom_site.calc_attached_atom
_definition.id '_atom_site.calc_attached_atom'
loop_
_alias.definition_id
'_atom_site.calc_attached_atom'
'_atom_site_calc_attached_atom'
_definition.update 2012-11-20
_description.text
;
The _atom_site.label of the atom site to which the 'geometry-
calculated' atom site is attached.
;
_name.category_id atom_site
_name.object_id calc_attached_atom
_name.linked_item_id '_atom_site.label'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
save_
save__atom_site.calc_flag
_definition.id '_atom_site.calc_flag'
loop_
_alias.definition_id
'_atom_site.calc_flag'
'_atom_site_calc_flag'
_definition.update 2012-11-20
_description.text
;
A standard code to signal if the site coordinates have been
determined from the intensities or calculated from the geometry
of surrounding sites, or have been assigned dummy coordinates.
;
_name.category_id atom_site
_name.object_id calc_flag
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
d 'determined from diffraction measurements'
calc 'calculated from molecular geometry'
c 'abbreviation for "calc"'
dum 'dummy site with meaningless coordinates'
_enumeration.default d
save_
save__atom_site.Cartn_x
_definition.id '_atom_site.Cartn_x'
loop_
_alias.definition_id
'_atom_site.Cartn_x'
'_atom_site_Cartn_x'
_name.category_id atom_site
_name.object_id Cartn_x
_type.contents Real
_type.purpose Measurand
_description.text
;
The atom site coordinates in angstroms specified according to a
set of orthogonal Cartesian axes related to the cell axes as
specified by the _atom_sites_Cartn_transform.axes description.
;
_enumeration.range -1000.:1000.
_type.source Derived
_type.container Single
_definition.update 2012-05-07
_units.code angstroms
save_
save__atom_site.Cartn_x_su
_definition.id '_atom_site.Cartn_x_su'
loop_
_alias.definition_id
'_atom_site.Cartn_x_su'
'_atom_site_Cartn_x_su'
'_atom_site.Cartn_x_esd'
_name.category_id atom_site
_name.object_id Cartn_x_su
_name.linked_item_id '_atom_site.Cartn_x'
_type.contents Real
_type.purpose SU
_description.text
;
Standard uncertainty values of the atom site coordinates
in angstroms specified according to a
set of orthogonal Cartesian axes related to the cell axes as
specified by the _atom_sites_Cartn_transform.axes description.
;
_enumeration.range -1000.:1000.
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code angstroms
save_
save__atom_site.Cartn_xyz
_definition.id '_atom_site.Cartn_xyz'
loop_
_alias.definition_id
'_atom_site.Cartn_xyz'
_definition.update 2012-11-20
_description.text
;
Vector of Cartesian (orthogonal angstrom) atom site coordinates.
;
_name.category_id atom_site
_name.object_id Cartn_xyz
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With a as atom_site
_atom_site.Cartn_xyz = [a.Cartn_x, a.Cartn_y, a.Cartn_z]
;
save_
save__atom_site.Cartn_y
_definition.id '_atom_site.Cartn_y'
loop_
_alias.definition_id
'_atom_site.Cartn_y'
'_atom_site_Cartn_y'
_name.category_id atom_site
_name.object_id Cartn_y
_type.contents Real
_type.purpose Measurand
_description.text
;
The atom site coordinates in angstroms specified according to a
set of orthogonal Cartesian axes related to the cell axes as
specified by the _atom_sites_Cartn_transform.axes description.
;
_enumeration.range -1000.:1000.
_type.source Derived
_type.container Single
_definition.update 2012-05-07
_units.code angstroms
save_
save__atom_site.Cartn_y_su
_definition.id '_atom_site.Cartn_y_su'
loop_
_alias.definition_id
'_atom_site.Cartn_y_su'
'_atom_site_Cartn_y_su'
'_atom_site.Cartn_y_esd'
_name.category_id atom_site
_name.object_id Cartn_y_su
_name.linked_item_id '_atom_site.Cartn_y'
_type.contents Real
_type.purpose SU
_description.text
;
Standard uncertainty values of the atom site coordinates
in angstroms specified according to a
set of orthogonal Cartesian axes related to the cell axes as
specified by the _atom_sites_Cartn_transform.axes description.
;
_enumeration.range -1000.:1000.
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code angstroms
save_
save__atom_site.Cartn_z
_definition.id '_atom_site.Cartn_z'
loop_
_alias.definition_id
'_atom_site.Cartn_z'
'_atom_site_Cartn_z'
_name.category_id atom_site
_name.object_id Cartn_z
_type.contents Real
_type.purpose Measurand
_description.text
;
The atom site coordinates in angstroms specified according to a
set of orthogonal Cartesian axes related to the cell axes as
specified by the _atom_sites_Cartn_transform.axes description.
;
_enumeration.range -1000.:1000.
_type.source Derived
_type.container Single
_definition.update 2012-05-07
_units.code angstroms
save_
save__atom_site.Cartn_z_su
_definition.id '_atom_site.Cartn_z_su'
loop_
_alias.definition_id
'_atom_site.Cartn_z_su'
'_atom_site_Cartn_z_su'
'_atom_site.Cartn_z_esd'
_name.category_id atom_site
_name.object_id Cartn_z_su
_name.linked_item_id '_atom_site.Cartn_z'
_type.contents Real
_type.purpose SU
_description.text
;
Standard uncertainty values of the atom site coordinates
in angstroms specified according to a
set of orthogonal Cartesian axes related to the cell axes as
specified by the _atom_sites_Cartn_transform.axes description.
;
_enumeration.range -1000.:1000.
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code angstroms
save_
save__atom_site.chemical_conn_number
_definition.id '_atom_site.chemical_conn_number'
loop_
_alias.definition_id
'_atom_site.chemical_conn_number'
'_atom_site_chemical_conn_number'
_definition.update 2012-11-20
_description.text
;
This number links an atom site to the chemical connectivity list.
It must match a number specified by _chemical_conn_atom.number.
;
_name.category_id atom_site
_name.object_id chemical_conn_number
_name.linked_item_id '_chemical_conn_atom.number'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Index
_enumeration.range 1:
save_
save__atom_site.constraints
_definition.id '_atom_site.constraints'
loop_
_alias.definition_id
'_atom_site.constraints'
'_atom_site_constraints'
_definition.update 2012-11-20
_description.text
;
A description of the constraints applied to parameters at this
site during refinement. See also _atom_site.refinement_flags
and _refine_ls.number_constraints.
;
_name.category_id atom_site
_name.object_id constraints
_type.purpose Encode
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
pop=1.0-pop(Zn3)
save_
save__atom_site.description
_definition.id '_atom_site.description'
loop_
_alias.definition_id
'_atom_site.description'
'_atom_site_description'
'_atom_site.details'
_definition.update 2012-11-20
_description.text
;
A description of special aspects of this site. See also
_atom_site.refinement_flags.
;
_name.category_id atom_site
_name.object_id description
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'Ag/Si disordered'
save_
save__atom_site.disorder_assembly
_definition.id '_atom_site.disorder_assembly'
loop_
_alias.definition_id
'_atom_site.disorder_assembly'
'_atom_site_disorder_assembly'
_definition.update 2012-11-20
_description.text
;
A code which identifies a cluster of atoms that show long range
positional disorder but are locally ordered. Within each such
cluster of atoms, _atom_site.disorder_group is used to identify
the sites that are simultaneously occupied. This field is only
needed if there is more than one cluster of disordered atoms
showing independent local order.
;
_name.category_id atom_site
_name.object_id disorder_assembly
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_description_example.case
_description_example.detail
A 'disordered methyl assembly with groups 1 and 2'
B 'disordered sites related by a mirror'
S 'disordered sites independent of symmetry'
save_
save__atom_site.disorder_group
_definition.id '_atom_site.disorder_group'
loop_
_alias.definition_id
'_atom_site.disorder_group'
'_atom_site_disorder_group'
_definition.update 2012-11-20
_description.text
;
A code that identifies a group of positionally disordered atom
sites that are locally simultaneously occupied. Atoms that are
positionally disordered over two or more sites (e.g. the H
atoms of a methyl group that exists in two orientations) can
be assigned to two or more groups. Sites belonging to the same
group are simultaneously occupied, but those belonging to
different groups are not. A minus prefix (e.g. "-1") is used to
indicate sites disordered about a special position.
;
_name.category_id atom_site
_name.object_id disorder_group
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_description_example.case
_description_example.detail
1 'unique disordered site in group 1'
2 'unique disordered site in group 2'
-1 'symmetry-independent disordered site'
save_
save__atom_site.fract_x
_definition.id '_atom_site.fract_x'
loop_
_alias.definition_id
'_atom_site.fract_x'
'_atom_site_fract_x'
_name.category_id atom_site
_name.object_id fract_x
_type.contents Real
_type.purpose Measurand
_description.text
;
Atom site coordinates as fractions of the cell length values.
;
_enumeration.range -1.:1.
_type.source Derived
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__atom_site.fract_x_su
_definition.id '_atom_site.fract_x_su'
loop_
_alias.definition_id
'_atom_site.fract_x_su'
'_atom_site_fract_x_su'
'_atom_site.fract_x_esd'
_name.category_id atom_site
_name.object_id fract_x_su
_name.linked_item_id '_atom_site.fract_x'
_type.contents Real
_type.purpose SU
_description.text
;
Standard uncertainty value of the atom site coordinates
as fractions of the cell length values.
;
_enumeration.range -1.:1.
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code none
save_
save__atom_site.fract_xyz
_definition.id '_atom_site.fract_xyz'
loop_
_alias.definition_id
'_atom_site.fract_xyz'
_definition.update 2012-11-20
_description.text
;
Vector of atom site coordinates projected onto the crystal unit
cell as fractions of the cell lengths.
;
_name.category_id atom_site
_name.object_id fract_xyz
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With a as atom_site
_atom_site.fract_xyz = [a.fract_x, a.fract_y, a.fract_z]
;
save_
save__atom_site.fract_y
_definition.id '_atom_site.fract_y'
loop_
_alias.definition_id
'_atom_site.fract_y'
'_atom_site_fract_y'
_name.category_id atom_site
_name.object_id fract_y
_type.contents Real
_type.purpose Measurand
_description.text
;
Atom site coordinates as fractions of the cell length values.
;
_enumeration.range -1.:1.
_type.source Derived
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__atom_site.fract_y_su
_definition.id '_atom_site.fract_y_su'
loop_
_alias.definition_id
'_atom_site.fract_y_su'
'_atom_site_fract_y_su'
'_atom_site.fract_y_esd'
_name.category_id atom_site
_name.object_id fract_y_su
_name.linked_item_id '_atom_site.fract_y'
_type.contents Real
_type.purpose SU
_description.text
;
Standard uncertainty value of the atom site coordinates
as fractions of the cell length values.
;
_enumeration.range -1.:1.
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code none
save_
save__atom_site.fract_z
_definition.id '_atom_site.fract_z'
loop_
_alias.definition_id
'_atom_site.fract_z'
'_atom_site_fract_z'
_name.category_id atom_site
_name.object_id fract_z
_type.contents Real
_type.purpose Measurand
_description.text
;
Atom site coordinates as fractions of the cell length values.
;
_enumeration.range -1.:1.
_type.source Derived
_type.container Single
_definition.update 2012-05-07
_units.code none
save_
save__atom_site.fract_z_su
_definition.id '_atom_site.fract_z_su'
loop_
_alias.definition_id
'_atom_site.fract_z_su'
'_atom_site_fract_z_su'
'_atom_site.fract_z_esd'
_name.category_id atom_site
_name.object_id fract_z_su
_name.linked_item_id '_atom_site.fract_z'
_type.contents Real
_type.purpose SU
_description.text
;
Standard uncertainty value of the atom site coordinates
as fractions of the cell length values.
;
_enumeration.range -1.:1.
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code none
save_
save__atom_site.key
_definition.id '_atom_site.key'
loop_
_alias.definition_id
'_atom_site.key'
_definition.update 2012-11-20
_description.text
;
Value is a unique key to a set of ATOM_SITE items
in a looped list.
;
_name.category_id atom_site
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _atom_site.key = _atom_site.label'
save_
save__atom_site.label
_definition.id '_atom_site.label'
loop_
_alias.definition_id
'_atom_site.label'
'_atom_site_label'
'_atom_site.id'
_name.category_id atom_site
_name.object_id label
_type.contents Code
_type.purpose Encode
_description.text
;
This label is a unique identifier for a particular site in the
asymmetric unit of the crystal unit cell. It is made up of
components, _atom_site.label_component_0 to *_6, which may be
specified as separate data items. Component 0 usually matches one
of the specified _atom_type.symbol codes. This is not mandatory
if an _atom_site.type_symbol item is included in the atom site
list. The _atom_site.type_symbol always takes precedence over
an _atom_site.label in the identification of the atom type. The
label components 1 to 6 are optional, and normally only
components 0 and 1 are used. Note that components 0 and 1 are
concatenated, while all other components, if specified, are
separated by an underline character. Underline separators are
only used if higher-order components exist. If an intermediate
component is not used it may be omitted provided the underline
separators are inserted. For example the label 'C233__ggg' is
acceptable and represents the components C, 233, '', and ggg.
Each label may have a different number of components.
;
_type.source Assigned
_name.linked_item_id '_atom_site.label'
_type.container Single
_definition.update 2012-10-16
loop_
_description_example.case
C12
Ca3g28
Fe3+17
H*251
C_a_phe_83_a_0
Zn_Zn_301_A_0
save_
save__atom_site.label_component_0
_definition.id '_atom_site.label_component_0'
loop_
_alias.definition_id
'_atom_site.label_component_0'
'_atom_site_label_component_0'
_name.category_id atom_site
_name.object_id label_component_0
_type.contents Code
_type.purpose Encode
_description.text
;
Component_0 is normally a code which matches identically with
one of the _atom_type.symbol codes. If this is the case then the
rules governing the _atom_type.symbol code apply. If, however,
the data item _atom_site.type_symbol is also specified in the
atom site list, component 0 need not match this symbol or adhere
to any of the _atom_type.symbol rules.
Component_1 is referred to as the "atom number". When component 0
is the atom type code, it is used to number the sites with the
same atom type. This component code must start with at least one
digit which is not followed by a + or - sign (to distinguish it
from the component 0 rules).
Components_2 to 6 contain the identifier, residue, sequence,
asymmetry identifier and alternate codes, respectively. These
codes may be composed of any characters except an underline.
;
_type.source Assigned
_type.container Single
_definition.update 2012-05-07
save_
save__atom_site.label_component_1
_definition.id '_atom_site.label_component_1'
loop_
_alias.definition_id
'_atom_site.label_component_1'
'_atom_site_label_component_1'
_name.category_id atom_site
_name.object_id label_component_1
_type.contents Code
_type.purpose Encode
_description.text
;
See label_component_0 description.
;
_type.source Assigned
_type.container Single
_definition.update 2012-05-07
save_
save__atom_site.label_component_2
_definition.id '_atom_site.label_component_2'
loop_
_alias.definition_id
'_atom_site.label_component_2'
'_atom_site_label_component_2'
_name.category_id atom_site
_name.object_id label_component_2
_type.contents Code
_type.purpose Encode
_description.text
;
See label_component_0 description.
;
_type.source Assigned
_type.container Single
_definition.update 2012-05-07
save_
save__atom_site.label_component_3
_definition.id '_atom_site.label_component_3'
loop_
_alias.definition_id
'_atom_site.label_component_3'
'_atom_site_label_component_3'
_name.category_id atom_site
_name.object_id label_component_3
_type.contents Code
_type.purpose Encode
_description.text
;
See label_component_0 description.
;
_type.source Assigned
_type.container Single
_definition.update 2012-05-07
save_
save__atom_site.label_component_4
_definition.id '_atom_site.label_component_4'
loop_
_alias.definition_id
'_atom_site.label_component_4'
'_atom_site_label_component_4'
_name.category_id atom_site
_name.object_id label_component_4
_type.contents Code
_type.purpose Encode
_description.text
;
See label_component_0 description.
;
_type.source Assigned
_type.container Single
_definition.update 2012-05-07
save_
save__atom_site.label_component_5
_definition.id '_atom_site.label_component_5'
loop_
_alias.definition_id
'_atom_site.label_component_5'
'_atom_site_label_component_5'
_name.category_id atom_site
_name.object_id label_component_5
_type.contents Code
_type.purpose Encode
_description.text
;
See label_component_0 description.
;
_type.source Assigned
_type.container Single
_definition.update 2012-05-07
save_
save__atom_site.label_component_6
_definition.id '_atom_site.label_component_6'
loop_
_alias.definition_id
'_atom_site.label_component_6'
'_atom_site_label_component_6'
_name.category_id atom_site
_name.object_id label_component_6
_type.contents Code
_type.purpose Encode
_description.text
;
See label_component_0 description.
;
_type.source Assigned
_type.container Single
_definition.update 2012-05-07
save_
save__atom_site.occupancy
_definition.id '_atom_site.occupancy'
loop_
_alias.definition_id
'_atom_site.occupancy'
'_atom_site_occupancy'
_definition.update 2012-11-20
_description.text
;
The fraction of the atom type present at this site.
The sum of the occupancies of all the atom types at this site
may not significantly exceed 1.0 unless it is a dummy site. The
value must lie in the 99.97% Gaussian confidence interval
-3u =< x =< 1 + 3u. The _enumeration.range of 0.0:1.0 is thus
correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u).
;
_name.category_id atom_site
_name.object_id occupancy
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_enumeration.default 1.0
_units.code none
save_
save__atom_site.occupancy_su
_definition.id '_atom_site.occupancy_su'
loop_
_alias.definition_id
'_atom_site.occupancy_su'
'_atom_site_occupancy_su'
'_atom_site.occupancy_esd'
_definition.update 2012-11-20
_description.text
;
Standard Uncertainty value for the
The fraction of the atom type present at this site.
;
_name.category_id atom_site
_name.object_id occupancy_su
_name.linked_item_id '_atom_site.occupancy'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_enumeration.default 0.0
_units.code none
save_
save__atom_site.refinement_flags
_definition.id '_atom_site.refinement_flags'
loop_
_alias.definition_id
'_atom_site.refinement_flags'
'_atom_site_refinement_flags'
_definition.update 2013-03-08
_description.text
;
A concatenated series of single-letter codes which indicate the
refinement restraints or constraints applied to this site.
;
_name.category_id atom_site
_name.object_id refinement_flags
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
S 'special position constraint on site'
G 'rigid group refinement of site'
R 'riding-atom site attached to non-riding atom'
D 'distance or angle restraint on site'
T 'thermal displacement constraints'
U 'Uiso or Uij restraint (rigid bond)'
P 'partial occupancy constraint'
. 'no refinement constraints'
_enumeration.default .
save_
save__atom_site.refinement_flags_adp
_definition.id '_atom_site.refinement_flags_adp'
loop_
_alias.definition_id
'_atom_site.refinement_flags_adp'
'_atom_site_refinement_flags_adp'
_definition.update 2012-11-20
_description.text
;
A code which indicates the refinement restraints or constraints
applied to the atomic displacement parameters of this site.
;
_name.category_id atom_site
_name.object_id refinement_flags_adp
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
. 'no constraints on atomic displacement parameters'
T 'special-position constraints on atomic displacement parameters'
U 'Uiso or Uij restraint (rigid bond)'
TU 'both constraints applied'
_enumeration.default .
save_
save__atom_site.refinement_flags_occupancy
_definition.id '_atom_site.refinement_flags_occupancy'
loop_
_alias.definition_id
'_atom_site.refinement_flags_occupancy'
'_atom_site_refinement_flags_occupancy'
_definition.update 2012-11-20
_description.text
;
A code which indicates the refinement restraints or constraints
applied to the occupancy of this site.
;
_name.category_id atom_site
_name.object_id refinement_flags_occupancy
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
. 'no constraints on atomic displacement parameters'
T 'special-position constraints on atomic displacement parameters'
U 'Uiso or Uij restraint (rigid bond)'
TU 'both constraints applied'
_enumeration.default .
save_
save__atom_site.refinement_flags_posn
_definition.id '_atom_site.refinement_flags_posn'
loop_
_alias.definition_id
'_atom_site.refinement_flags_posn'
'_atom_site_refinement_flags_posn'
_definition.update 2012-11-20
_description.text
;
A code which indicates the refinement restraints or constraints
applied to the positional coordinates of this site.
;
_name.category_id atom_site
_name.object_id refinement_flags_posn
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
. 'no constraints on positional coordinates'
D 'distance or angle restraint on positional coordinates'
G 'rigid-group refinement of positional coordinates'
R 'riding-atom site attached to non-riding atom'
S 'special-position constraint on positional coordinates'
DG 'combination of the above constraints'
DR 'combination of the above constraints'
DS 'combination of the above constraints'
GR 'combination of the above constraints'
GS 'combination of the above constraints'
RS 'combination of the above constraints'
DGR 'combination of the above constraints'
DGS 'combination of the above constraints'
DRS 'combination of the above constraints'
GRS 'combination of the above constraints'
DGRS 'combination of the above constraints'
_enumeration.default .
save_
save__atom_site.restraints
_definition.id '_atom_site.restraints'
loop_
_alias.definition_id
'_atom_site.restraints'
'_atom_site_restraints'
_definition.update 2012-11-20
_description.text
;
A description of restraints applied to specific parameters at
this site during refinement. See also _atom_site.refinement_flags
and _refine_ls.number_restraints.
;
_name.category_id atom_site
_name.object_id restraints
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'restrained to planar ring'
save_
save__atom_site.site_symmetry_multiplicity
_definition.id '_atom_site.site_symmetry_multiplicity'
loop_
_alias.definition_id
'_atom_site.site_symmetry_multiplicity'
'_atom_site_site_symmetry_multiplicity'
'_atom_site_symmetry_multiplicity'
'_atom_site.symmetry_multiplicity'
_definition.update 2013-04-28
_description.text
;
The number of different sites that are generated by the
application of the space-group symmetry to the coordinates
given for this site. It is equal to the multiplicity given
for this Wyckoff site in International Tables for Cryst.
Vol. A (2002). It is equal to the multiplicity of the general
position divided by the order of the site symmetry given in
_atom_site.site_symmetry_order.
;
_name.category_id atom_site
_name.object_id site_symmetry_multiplicity
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Index
_enumeration.range 1:192
loop_
_method.purpose
_method.expression
Evaluation
;
With a as atom_site
mul = 0
xyz = a.fract_xyz
Loop s as symmetry_equiv {
sxyz = s.R * xyz + s.T
diff = Mod( 99.5 + xyz - sxyz, 1.0) - 0.5
If ( Norm ( diff ) < 0.1 ) mul += 1
}
_atom_site.site_symmetry_multiplicity = _symmetry.multiplicity / mul
;
save_
save__atom_site.site_symmetry_order
_definition.id '_atom_site.site_symmetry_order'
loop_
_alias.definition_id
'_atom_site.site_symmetry_order'
'_atom_site_site_symmetry_order'
_definition.update 2012-11-20
_description.text
;
The number of times application of the crystallographic symmetry
to the coordinates for this site generates the same coordinates.
That is:
multiplicity of the general position
------------------------------------
_atom_site.site_symmetry_multiplicity
;
_name.category_id atom_site
_name.object_id site_symmetry_order
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Index
_enumeration.range 1:48
save_
save__atom_site.tensor_beta
_definition.id '_atom_site.tensor_beta'
loop_
_alias.definition_id
'_atom_site.tensor_beta'
_definition.update 2013-04-28
_description.text
;
The symmetric anisotropic atomic displacement tensor beta[I,J]
appears in a structure factor expression as:
t = exp -[ beta11 h h + ............ 2 beta23 k l ]
It is related to the adp matrices U(IJ) and B(IJ) as follows:
t = exp -2pi**2 ( U11 h h a* a* + ...... 2 U23 k l b* c* )
t = exp - 0.25 ( B11 h h a* a* + ...... 2 B23 k l b* c* )
;
_name.category_id atom_site
_name.object_id tensor_beta
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3 3]
loop_
_method.purpose
_method.expression
Evaluation
;
With a as atom_site
label = a.label
If (a.adp_type == 'uani') {
Loop b as atom_site_aniso {
If(label == b.label) {
UIJ = b.matrix_U
Break
} } }
Else If (a.adp_type == 'bani') {
Loop b as atom_site_aniso {
If(label == b.label) {
UIJ = b.matrix_B / (8 * Pi**2)
Break
} } }
Else {
If (a.adp_type == 'uiso') U = a.U_iso_or_equiv
Else U = a.B_iso_or_equiv / (8 * Pi**2)
UIJ = U * _cell_reciprocal.convert_Uiso_to_Uij
}
CUB = _cell_reciprocal.convert_Uij_to_betaij
_atom_site.tensor_beta = CUB * UIJ * CUB
;
save_
save__atom_site.type_symbol
_definition.id '_atom_site.type_symbol'
loop_
_alias.definition_id
'_atom_site.type_symbol'
'_atom_site_type_symbol'
_definition.update 2012-11-20
_description.text
;
A code to identify the atom specie(s) occupying this site.
This code must match a corresponding _atom_type.symbol. The
specification of this code is optional if component_0 of the
_atom_site.label is used for this purpose. See _atom_type.symbol.
;
_name.category_id atom_site
_name.object_id type_symbol
_name.linked_item_id '_atom_type.symbol'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
loop_
_description_example.case
Cu
Cu2+
S
O1-
loop_
_method.purpose
_method.expression
Evaluation
;
_atom_site.type_symbol = AtomType ( _atom_site.label )
;
save_
save__atom_site.U_equiv_geom_mean
_definition.id '_atom_site.U_equiv_geom_mean'
loop_
_alias.definition_id
'_atom_site.U_equiv_geom_mean'
'_atom_site_U_equiv_geom_mean'
_definition.update 2012-11-20
_description.text
;
Equivalent isotropic atomic displacement parameter, U(equiv),
in angstroms squared, calculated as the geometric mean of
the anisotropic atomic displacement parameters.
U(equiv) = (U~i~ U~j~ U~k~)^1/3^
U~n~ = the principal components of the orthogonalised U^ij^
;
_name.category_id atom_site
_name.object_id U_equiv_geom_mean
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstrom_squared
save_
save__atom_site.U_equiv_geom_mean_su
_definition.id '_atom_site.U_equiv_geom_mean_su'
loop_
_alias.definition_id
'_atom_site.U_equiv_geom_mean_su'
'_atom_site_U_equiv_geom_mean_su'
'_atom_site.U_equiv_geom_mean_esd'
_definition.update 2012-11-20
_description.text
;
Standard uncertainty values (esds) of the U(equiv).
;
_name.category_id atom_site
_name.object_id U_equiv_geom_mean_su
_name.linked_item_id '_atom_site.U_equiv_geom_mean'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstrom_squared
save_
save__atom_site.U_iso_or_equiv
_definition.id '_atom_site.U_iso_or_equiv'
loop_
_alias.definition_id
'_atom_site.U_iso_or_equiv'
'_atom_site_U_iso_or_equiv'
_definition.update 2012-11-20
_description.text
;
Isotropic atomic displacement parameter, or equivalent isotropic
atomic displacement parameter, U(equiv), in angstroms squared,
calculated from anisotropic atomic displacement parameters.
U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~ a~j~)]
a = the real-space cell lengths
a* = the reciprocal-space cell lengths
Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
;
_name.category_id atom_site
_name.object_id U_iso_or_equiv
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstrom_squared
save_
save__atom_site.U_iso_or_equiv_su
_definition.id '_atom_site.U_iso_or_equiv_su'
loop_
_alias.definition_id
'_atom_site.U_iso_or_equiv_su'
'_atom_site_U_iso_or_equiv_su'
'_atom_site.U_iso_or_equiv_esd'
_definition.update 2012-11-20
_description.text
;
Standard uncertainty values (esds) of the U(iso) or U(equiv).
;
_name.category_id atom_site
_name.object_id U_iso_or_equiv_su
_name.linked_item_id '_atom_site.U_iso_or_equiv'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstrom_squared
save_
save__atom_site.Wyckoff_symbol
_definition.id '_atom_site.Wyckoff_symbol'
loop_
_alias.definition_id
'_atom_site.Wyckoff_symbol'
'_atom_site_Wyckoff_symbol'
_definition.update 2012-11-20
_description.text
;
The Wyckoff symbol (letter) as listed in the space-group section
of International Tables for Crystallography, Vol. A (1987).
;
_name.category_id atom_site
_name.object_id Wyckoff_symbol
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save_ATOM_SITE_ANISO
_definition.id ATOM_SITE_ANISO
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to describe the anisotropic
thermal parameters of the atomic sites in a crystal structure.
;
_name.category_id ATOM_SITE
_name.object_id ATOM_SITE_ANISO
_category.key_id '_atom_site_aniso.key'
_category.key_list ['_atom_site_aniso.label']
save_
save__atom_site_aniso.B_11
_definition.id '_atom_site_aniso.B_11'
loop_
_alias.definition_id
'_atom_site_aniso.B_11'
'_atom_site_aniso_B_11'
'_atom_site.aniso_B[1][1]'
'_atom_site_anisotrop.B[1][1]'
_name.category_id atom_site_aniso
_name.object_id B_11
_type.contents Real
_type.purpose Measurand
_description.text
;
These are the standard anisotropic atomic displacement components
in angstroms squared which appear in the structure factor term:
T = exp{-1/4 sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
The unique elements of the real symmetric matrix are entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2013-03-08
_units.code angstrom_squared
save_
save__atom_site_aniso.B_11_su
_definition.id '_atom_site_aniso.B_11_su'
loop_
_alias.definition_id
'_atom_site_aniso.B_11_su'
'_atom_site_aniso_B_11_su'
'_atom_site.aniso_B[1][1]_esd'
'_atom_site_anisotrop.B[1][1]_esd'
_name.category_id atom_site_aniso
_name.object_id B_11_su
_name.linked_item_id '_atom_site_aniso.B_11'
_type.contents Real
_type.purpose SU
_description.text
;
These are the standard uncertainty values (SU) for the standard
form of the Bij anisotropic atomic displacement components (see
_aniso_BIJ. Because these values are TYPE measurand, the su values
may in practice be auto generated as part of the Bij calculation.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code angstrom_squared
save_
save__atom_site_aniso.B_12
_definition.id '_atom_site_aniso.B_12'
loop_
_alias.definition_id
'_atom_site_aniso.B_12'
'_atom_site_aniso_B_12'
'_atom_site.aniso_B[1][2]'
'_atom_site_anisotrop.B[1][2]'
_name.category_id atom_site_aniso
_name.object_id B_12
_type.contents Real
_type.purpose Measurand
_description.text
;
These are the standard anisotropic atomic displacement components
in angstroms squared which appear in the structure factor term:
T = exp{-1/4 sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
The unique elements of the real symmetric matrix are entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2013-03-08
_units.code angstrom_squared
save_
save__atom_site_aniso.B_12_su
_definition.id '_atom_site_aniso.B_12_su'
loop_
_alias.definition_id
'_atom_site_aniso.B_12_su'
'_atom_site_aniso_B_12_su'
'_atom_site.aniso_B[1][2]_esd'
'_atom_site_anisotrop.B[1][2]_esd'
_name.category_id atom_site_aniso
_name.object_id B_12_su
_name.linked_item_id '_atom_site_aniso.B_12'
_type.contents Real
_type.purpose SU
_description.text
;
These are the standard uncertainty values (SU) for the standard
form of the Bij anisotropic atomic displacement components (see
_aniso_BIJ. Because these values are TYPE measurand, the su values
may in practice be auto generated as part of the Bij calculation.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code angstrom_squared
save_
save__atom_site_aniso.B_13
_definition.id '_atom_site_aniso.B_13'
loop_
_alias.definition_id
'_atom_site_aniso.B_13'
'_atom_site_aniso_B_13'
'_atom_site.aniso_B[1][3]'
'_atom_site_anisotrop.B[1][3]'
_name.category_id atom_site_aniso
_name.object_id B_13
_type.contents Real
_type.purpose Measurand
_description.text
;
These are the standard anisotropic atomic displacement components
in angstroms squared which appear in the structure factor term:
T = exp{-1/4 sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
The unique elements of the real symmetric matrix are entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2013-03-08
_units.code angstrom_squared
save_
save__atom_site_aniso.B_13_su
_definition.id '_atom_site_aniso.B_13_su'
loop_
_alias.definition_id
'_atom_site_aniso.B_13_su'
'_atom_site_aniso_B_13_su'
'_atom_site.aniso_B[1][3]_esd'
'_atom_site_anisotrop.B[1][3]_esd'
_name.category_id atom_site_aniso
_name.object_id B_13_su
_name.linked_item_id '_atom_site_aniso.B_13'
_type.contents Real
_type.purpose SU
_description.text
;
These are the standard uncertainty values (SU) for the standard
form of the Bij anisotropic atomic displacement components (see
_aniso_BIJ. Because these values are TYPE measurand, the su values
may in practice be auto generated as part of the Bij calculation.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code angstrom_squared
save_
save__atom_site_aniso.B_22
_definition.id '_atom_site_aniso.B_22'
loop_
_alias.definition_id
'_atom_site_aniso.B_22'
'_atom_site_aniso_B_22'
'_atom_site.aniso_B[2][2]'
'_atom_site_anisotrop.B[2][2]'
_name.category_id atom_site_aniso
_name.object_id B_22
_type.contents Real
_type.purpose Measurand
_description.text
;
These are the standard anisotropic atomic displacement components
in angstroms squared which appear in the structure factor term:
T = exp{-1/4 sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
The unique elements of the real symmetric matrix are entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2013-03-08
_units.code angstrom_squared
save_
save__atom_site_aniso.B_22_su
_definition.id '_atom_site_aniso.B_22_su'
loop_
_alias.definition_id
'_atom_site_aniso.B_22_su'
'_atom_site_aniso_B_22_su'
'_atom_site.aniso_B[2][2]_esd'
'_atom_site_anisotrop.B[2][2]_esd'
_name.category_id atom_site_aniso
_name.object_id B_22_su
_name.linked_item_id '_atom_site_aniso.B_22'
_type.contents Real
_type.purpose SU
_description.text
;
These are the standard uncertainty values (SU) for the standard
form of the Bij anisotropic atomic displacement components (see
_aniso_BIJ. Because these values are TYPE measurand, the su values
may in practice be auto generated as part of the Bij calculation.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code angstrom_squared
save_
save__atom_site_aniso.B_23
_definition.id '_atom_site_aniso.B_23'
loop_
_alias.definition_id
'_atom_site_aniso.B_23'
'_atom_site_aniso_B_23'
'_atom_site.aniso_B[2][3]'
'_atom_site_anisotrop.B[2][3]'
_name.category_id atom_site_aniso
_name.object_id B_23
_type.contents Real
_type.purpose Measurand
_description.text
;
These are the standard anisotropic atomic displacement components
in angstroms squared which appear in the structure factor term:
T = exp{-1/4 sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
The unique elements of the real symmetric matrix are entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2013-03-08
_units.code angstrom_squared
save_
save__atom_site_aniso.B_23_su
_definition.id '_atom_site_aniso.B_23_su'
loop_
_alias.definition_id
'_atom_site_aniso.B_23_su'
'_atom_site_aniso_B_23_su'
'_atom_site.aniso_B[2][3]_esd'
'_atom_site_anisotrop.B[2][3]_esd'
_name.category_id atom_site_aniso
_name.object_id B_23_su
_name.linked_item_id '_atom_site_aniso.B_23'
_type.contents Real
_type.purpose SU
_description.text
;
These are the standard uncertainty values (SU) for the standard
form of the Bij anisotropic atomic displacement components (see
_aniso_BIJ. Because these values are TYPE measurand, the su values
may in practice be auto generated as part of the Bij calculation.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code angstrom_squared
save_
save__atom_site_aniso.B_33
_definition.id '_atom_site_aniso.B_33'
loop_
_alias.definition_id
'_atom_site_aniso.B_33'
'_atom_site_aniso_B_33'
'_atom_site.aniso_B[3][3]'
'_atom_site_anisotrop.B[3][3]'
_name.category_id atom_site_aniso
_name.object_id B_33
_type.contents Real
_type.purpose Measurand
_description.text
;
These are the standard anisotropic atomic displacement components
in angstroms squared which appear in the structure factor term:
T = exp{-1/4 sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
The unique elements of the real symmetric matrix are entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2013-03-08
_units.code angstrom_squared
save_
save__atom_site_aniso.B_33_su
_definition.id '_atom_site_aniso.B_33_su'
loop_
_alias.definition_id
'_atom_site_aniso.B_33_su'
'_atom_site_aniso_B_33_su'
'_atom_site.aniso_B[3][3]_esd'
'_atom_site_anisotrop.B[3][3]_esd'
_name.category_id atom_site_aniso
_name.object_id B_33_su
_name.linked_item_id '_atom_site_aniso.B_33'
_type.contents Real
_type.purpose SU
_description.text
;
These are the standard uncertainty values (SU) for the standard
form of the Bij anisotropic atomic displacement components (see
_aniso_BIJ. Because these values are TYPE measurand, the su values
may in practice be auto generated as part of the Bij calculation.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code angstrom_squared
save_
save__atom_site_aniso.key
_definition.id '_atom_site_aniso.key'
loop_
_alias.definition_id
'_atom_site_aniso.key'
_definition.update 2012-11-20
_description.text
;
Value is a unique key to a set of ATOM_SITE_ANISO items
in a looped list.
;
_name.category_id atom_site_aniso
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _atom_site_aniso.key = _atom_site_aniso.label'
save_
save__atom_site_aniso.label
_definition.id '_atom_site_aniso.label'
loop_
_alias.definition_id
'_atom_site_aniso.label'
'_atom_site_aniso_label'
'_atom_site_anisotrop.id'
_definition.update 2013-01-23
_description.text
;
Anisotropic atomic displacement parameters are usually looped in
a separate list. If this is the case, this code must match the
_atom_site_label of the associated atom in the atom coordinate
list and conform with the same rules described in _atom_site.label.
;
_name.category_id atom_site_aniso
_name.object_id label
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__atom_site_aniso.matrix_B
_definition.id '_atom_site_aniso.matrix_B'
loop_
_alias.definition_id
'_atom_site_aniso.matrix_B'
_definition.update 2012-11-20
_description.text
;
The symmetric anisotropic atomic displacement matrix B.
;
_name.category_id atom_site_aniso
_name.object_id matrix_B
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3 3]
loop_
_method.purpose
_method.expression
Evaluation
;
With a as atom_site_aniso
a.matrix_B = [[ a.B_11, a.B_12, a.B_13 ],
[ a.B_12, a.B_22, a.B_23 ],
[ a.B_13, a.B_23, a.B_33 ]]
;
save_
save__atom_site_aniso.matrix_U
_definition.id '_atom_site_aniso.matrix_U'
loop_
_alias.definition_id
'_atom_site_aniso.matrix_U'
_definition.update 2012-11-20
_description.text
;
The symmetric anisotropic atomic displacement matrix U.
;
_name.category_id atom_site_aniso
_name.object_id matrix_U
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3 3]
loop_
_method.purpose
_method.expression
Evaluation
;
With a as atom_site_aniso
a.matrix_U = [[ a.U_11, a.U_12, a.U_13 ],
[ a.U_12, a.U_22, a.U_23 ],
[ a.U_13, a.U_23, a.U_33 ]]
;
save_
save__atom_site_aniso.ratio
_definition.id '_atom_site_aniso.ratio'
loop_
_alias.definition_id
'_atom_site_aniso.ratio'
'_atom_site_aniso_ratio'
'_atom_site_anisotrop.ratio'
'_atom_site.aniso_ratio'
_definition.update 2012-11-20
_description.text
;
Ratio of the maximum to minimum eigenvalues of the atomic
displacement (thermal) ellipsoids.
;
_name.category_id atom_site_aniso
_name.object_id ratio
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 1.0:
_units.code none
save_
save__atom_site_aniso.type_symbol
_definition.id '_atom_site_aniso.type_symbol'
loop_
_alias.definition_id
'_atom_site_aniso.type_symbol'
'_atom_site_aniso_type_symbol'
'_atom_site_anisotrop.type_symbol'
_definition.update 2012-11-20
_description.text
;
This _atom_type.symbol code links the anisotropic atom parameters to
the atom type data associated with this site and must match one of
the _atom_type.symbol codes in this list.
;
_name.category_id atom_site_aniso
_name.object_id type_symbol
_name.linked_item_id '_atom_type.symbol'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation
;
_atom_site_aniso.type_symbol = AtomType ( _atom_site_aniso.label )
;
save_
save__atom_site_aniso.U_11
_definition.id '_atom_site_aniso.U_11'
loop_
_alias.definition_id
'_atom_site_aniso.U_11'
'_atom_site_aniso_U_11'
'_atom_site.aniso_U[1][1]'
'_atom_site_anisotrop.U[1][1]'
_name.category_id atom_site_aniso
_name.object_id U_11
_type.contents Real
_type.purpose Measurand
_description.text
;
These are the standard anisotropic atomic displacement
components in angstroms squared which appear in the
structure factor term:
T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
The unique elements of the real symmetric matrix are entered by row.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2013-03-08
_units.code angstrom_squared
save_
save__atom_site_aniso.U_11_su
_definition.id '_atom_site_aniso.U_11_su'
loop_
_alias.definition_id
'_atom_site_aniso.U_11_su'
'_atom_site_aniso_U_11_su'
'_atom_site.aniso_U[1][1]_esd'
'_atom_site_anisotrop.U[1][1]_esd'
_name.category_id atom_site_aniso
_name.object_id U_11_su
_name.linked_item_id '_atom_site_aniso.U_11'
_type.contents Real
_type.purpose SU
_description.text
;
These are the standard uncertainty values (SU) for the standard
form of the Uij anisotropic atomic displacement components (see
_aniso_UIJ. Because these values are TYPE measurand, the su values
may in practice be auto generated as part of the Uij calculation.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code angstrom_squared
save_
save__atom_site_aniso.U_12
_definition.id '_atom_site_aniso.U_12'
loop_
_alias.definition_id
'_atom_site_aniso.U_12'
'_atom_site_aniso_U_12'
'_atom_site.aniso_U[1][2]'
'_atom_site_anisotrop.U[1][2]'
_name.category_id atom_site_aniso
_name.object_id U_12
_type.contents Real
_type.purpose Measurand
_description.text
;
These are the standard anisotropic atomic displacement
components in angstroms squared which appear in the
structure factor term:
T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
The unique elements of the real symmetric matrix are entered by row.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2013-03-08
_units.code angstrom_squared
save_
save__atom_site_aniso.U_12_su
_definition.id '_atom_site_aniso.U_12_su'
loop_
_alias.definition_id
'_atom_site_aniso.U_12_su'
'_atom_site_aniso_U_12_su'
'_atom_site.aniso_U[1][2]_esd'
'_atom_site_anisotrop.U[1][2]_esd'
_name.category_id atom_site_aniso
_name.object_id U_12_su
_name.linked_item_id '_atom_site_aniso.U_12'
_type.contents Real
_type.purpose SU
_description.text
;
These are the standard uncertainty values (SU) for the standard
form of the Uij anisotropic atomic displacement components (see
_aniso_UIJ. Because these values are TYPE measurand, the su values
may in practice be auto generated as part of the Uij calculation.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code angstrom_squared
save_
save__atom_site_aniso.U_13
_definition.id '_atom_site_aniso.U_13'
loop_
_alias.definition_id
'_atom_site_aniso.U_13'
'_atom_site_aniso_U_13'
'_atom_site.aniso_U[1][3]'
'_atom_site_anisotrop.U[1][3]'
_name.category_id atom_site_aniso
_name.object_id U_13
_type.contents Real
_type.purpose Measurand
_description.text
;
These are the standard anisotropic atomic displacement
components in angstroms squared which appear in the
structure factor term:
T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
The unique elements of the real symmetric matrix are entered by row.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2013-03-08
_units.code angstrom_squared
save_
save__atom_site_aniso.U_13_su
_definition.id '_atom_site_aniso.U_13_su'
loop_
_alias.definition_id
'_atom_site_aniso.U_13_su'
'_atom_site_aniso_U_13_su'
'_atom_site.aniso_U[1][3]_esd'
'_atom_site_anisotrop.U[1][3]_esd'
_name.category_id atom_site_aniso
_name.object_id U_13_su
_name.linked_item_id '_atom_site_aniso.U_13'
_type.contents Real
_type.purpose SU
_description.text
;
These are the standard uncertainty values (SU) for the standard
form of the Uij anisotropic atomic displacement components (see
_aniso_UIJ. Because these values are TYPE measurand, the su values
may in practice be auto generated as part of the Uij calculation.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code angstrom_squared
save_
save__atom_site_aniso.U_22
_definition.id '_atom_site_aniso.U_22'
loop_
_alias.definition_id
'_atom_site_aniso.U_22'
'_atom_site_aniso_U_22'
'_atom_site.aniso_U[2][2]'
'_atom_site_anisotrop.U[2][2]'
_name.category_id atom_site_aniso
_name.object_id U_22
_type.contents Real
_type.purpose Measurand
_description.text
;
These are the standard anisotropic atomic displacement
components in angstroms squared which appear in the
structure factor term:
T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
The unique elements of the real symmetric matrix are entered by row.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2013-03-08
_units.code angstrom_squared
save_
save__atom_site_aniso.U_22_su
_definition.id '_atom_site_aniso.U_22_su'
loop_
_alias.definition_id
'_atom_site_aniso.U_22_su'
'_atom_site_aniso_U_22_su'
'_atom_site.aniso_U[2][2]_esd'
'_atom_site_anisotrop.U[2][2]_esd'
_name.category_id atom_site_aniso
_name.object_id U_22_su
_name.linked_item_id '_atom_site_aniso.U_22'
_type.contents Real
_type.purpose SU
_description.text
;
These are the standard uncertainty values (SU) for the standard
form of the Uij anisotropic atomic displacement components (see
_aniso_UIJ. Because these values are TYPE measurand, the su values
may in practice be auto generated as part of the Uij calculation.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code angstrom_squared
save_
save__atom_site_aniso.U_23
_definition.id '_atom_site_aniso.U_23'
loop_
_alias.definition_id
'_atom_site_aniso.U_23'
'_atom_site_aniso_U_23'
'_atom_site.aniso_U[2][3]'
'_atom_site_anisotrop.U[2][3]'
_name.category_id atom_site_aniso
_name.object_id U_23
_type.contents Real
_type.purpose Measurand
_description.text
;
These are the standard anisotropic atomic displacement
components in angstroms squared which appear in the
structure factor term:
T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
The unique elements of the real symmetric matrix are entered by row.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2013-03-08
_units.code angstrom_squared
save_
save__atom_site_aniso.U_23_su
_definition.id '_atom_site_aniso.U_23_su'
loop_
_alias.definition_id
'_atom_site_aniso.U_23_su'
'_atom_site_aniso_U_23_su'
'_atom_site.aniso_U[2][3]_esd'
'_atom_site_anisotrop.U[2][3]_esd'
_name.category_id atom_site_aniso
_name.object_id U_23_su
_name.linked_item_id '_atom_site_aniso.U_23'
_type.contents Real
_type.purpose SU
_description.text
;
These are the standard uncertainty values (SU) for the standard
form of the Uij anisotropic atomic displacement components (see
_aniso_UIJ. Because these values are TYPE measurand, the su values
may in practice be auto generated as part of the Uij calculation.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code angstrom_squared
save_
save__atom_site_aniso.U_33
_definition.id '_atom_site_aniso.U_33'
loop_
_alias.definition_id
'_atom_site_aniso.U_33'
'_atom_site_aniso_U_33'
'_atom_site.aniso_U[3][3]'
'_atom_site_anisotrop.U[3][3]'
_name.category_id atom_site_aniso
_name.object_id U_33
_type.contents Real
_type.purpose Measurand
_description.text
;
These are the standard anisotropic atomic displacement
components in angstroms squared which appear in the
structure factor term:
T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
The unique elements of the real symmetric matrix are entered by row.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2013-03-08
_units.code angstrom_squared
save_
save__atom_site_aniso.U_33_su
_definition.id '_atom_site_aniso.U_33_su'
loop_
_alias.definition_id
'_atom_site_aniso.U_33_su'
'_atom_site_aniso_U_33_su'
'_atom_site.aniso_U[3][3]_esd'
'_atom_site_anisotrop.U[3][3]_esd'
_name.category_id atom_site_aniso
_name.object_id U_33_su
_name.linked_item_id '_atom_site_aniso.U_33'
_type.contents Real
_type.purpose SU
_description.text
;
These are the standard uncertainty values (SU) for the standard
form of the Uij anisotropic atomic displacement components (see
_aniso_UIJ. Because these values are TYPE measurand, the su values
may in practice be auto generated as part of the Uij calculation.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2014-06-08
_units.code angstrom_squared
save_
save_ATOM_SITES
_definition.id ATOM_SITES
_definition.scope Category
_definition.class Set
_definition.update 2012-11-20
_description.text
;
The CATEGORY of data items used to describe information which applies
to all atom sites in a crystal structure.
;
_name.category_id ATOM
_name.object_id ATOM_SITES
save_
save__atom_sites.solution_hydrogens
_definition.id '_atom_sites.solution_hydrogens'
loop_
_alias.definition_id
'_atom_sites.solution_hydrogens'
'_atom_sites_solution_hydrogens'
_definition.update 2012-11-20
_description.text
;
Codes which identify the methods used to locate the initial
atom sites. The *_primary code identifies how the first
atom sites were determined; the *_secondary code identifies
how the remaining non-hydrogen sites were located; and the
*_hydrogens code identifies how the hydrogen sites were located.
Ref: Sheldrick, G. M., Hauptman, H. A., Weeks, C. M.,
Miller, R. and Us\'on, I. (2001). Ab initio phasing.
In International Tables for Crystallography,
Vol. F. Crystallography of biological macromolecules,
edited by M. G. Rossmann and E. Arnold, ch. 16.1.
Dordrecht: Kluwer Academic Publishers.
;
_name.category_id atom_sites
_name.object_id solution_hydrogens
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
difmap 'difference Fourier map'
vecmap 'real-space vector search'
heavy 'heavy-atom method'
direct 'structure-invariant direct methods'
geom 'inferred from neighbouring sites'
disper 'anomalous-dispersion techniques'
isomor 'isomorphous structure methods'
notdet 'coordinates were not determined'
dual 'dual-space method (Sheldrick et al., 2001)'
iterative
;iterative e.g. charge flipping [Oszl\'anyi, G.
and S\"uto, A. (2004). Acta Cryst. A60, 134-141]
;
other 'a method not included elsewhere in this list'
_enumeration.default difmap
save_
save__atom_sites.solution_primary
_definition.id '_atom_sites.solution_primary'
loop_
_alias.definition_id
'_atom_sites.solution_primary'
'_atom_sites_solution_primary'
_definition.update 2012-11-20
_description.text
;
Codes which identify the methods used to locate the initial
atom sites. The *_primary code identifies how the first
atom sites were determined; the *_secondary code identifies
how the remaining non-hydrogen sites were located; and the
*_hydrogens code identifies how the hydrogen sites were located.
Ref: Sheldrick, G. M., Hauptman, H. A., Weeks, C. M.,
Miller, R. and Us\'on, I. (2001). Ab initio phasing.
In International Tables for Crystallography,
Vol. F. Crystallography of biological macromolecules,
edited by M. G. Rossmann and E. Arnold, ch. 16.1.
Dordrecht: Kluwer Academic Publishers.
;
_name.category_id atom_sites
_name.object_id solution_primary
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
difmap 'difference Fourier map'
vecmap 'real-space vector search'
heavy 'heavy-atom method'
direct 'structure-invariant direct methods'
geom 'inferred from neighbouring sites'
disper 'anomalous-dispersion techniques'
isomor 'isomorphous structure methods'
notdet 'coordinates were not determined'
dual 'dual-space method (Sheldrick et al., 2001)'
iterative
;iterative e.g. charge flipping [Oszl\'anyi, G.
and S\"uto, A. (2004). Acta Cryst. A60, 134-141]
;
other 'a method not included elsewhere in this list'
_enumeration.default direct
save_
save__atom_sites.solution_secondary
_definition.id '_atom_sites.solution_secondary'
loop_
_alias.definition_id
'_atom_sites.solution_secondary'
'_atom_sites_solution_secondary'
_definition.update 2012-11-20
_description.text
;
Codes which identify the methods used to locate the initial
atom sites. The *_primary code identifies how the first
atom sites were determined; the *_secondary code identifies
how the remaining non-hydrogen sites were located; and the
*_hydrogens code identifies how the hydrogen sites were located.
Ref: Sheldrick, G. M., Hauptman, H. A., Weeks, C. M.,
Miller, R. and Us\'on, I. (2001). Ab initio phasing.
In International Tables for Crystallography,
Vol. F. Crystallography of biological macromolecules,
edited by M. G. Rossmann and E. Arnold, ch. 16.1.
Dordrecht: Kluwer Academic Publishers.
;
_name.category_id atom_sites
_name.object_id solution_secondary
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
difmap 'difference Fourier map'
vecmap 'real-space vector search'
heavy 'heavy-atom method'
direct 'structure-invariant direct methods'
geom 'inferred from neighbouring sites'
disper 'anomalous-dispersion techniques'
isomor 'isomorphous structure methods'
notdet 'coordinates were not determined'
dual 'dual-space method (Sheldrick et al., 2001)'
iterative
;iterative e.g. charge flipping [Oszl\'anyi, G.
and S\"uto, A. (2004). Acta Cryst. A60, 134-141]
;
other 'a method not included elsewhere in this list'
_enumeration.default difmap
save_
save__atom_sites.special_details
_definition.id '_atom_sites.special_details'
loop_
_alias.definition_id
'_atom_sites.special_details'
'_atom_sites_special_details'
_definition.update 2012-11-20
_description.text
;
Information about atomic coordinates not coded elsewhere in the CIF.
;
_name.category_id atom_sites
_name.object_id special_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_ATOM_SITES_CARTN_TRANSFORM
_definition.id ATOM_SITES_CARTN_TRANSFORM
_definition.scope Category
_definition.class Set
_definition.update 2012-11-20
_description.text
;
The CATEGORY of data items used to describe the matrix elements
used to transform Cartesion coordinates into fractional coordinates
of all atom sites in a crystal structure.
;
_name.category_id ATOM_SITES
_name.object_id ATOM_SITES_CARTN_TRANSFORM
save_
save__atom_sites_Cartn_transform.axes
_definition.id '_atom_sites_Cartn_transform.axes'
loop_
_alias.definition_id
'_atom_sites_Cartn_transform.axes'
'_atom_sites_Cartn_transform_axes'
'_atom_sites.Cartn_transform_axes'
_definition.update 2012-12-11
_description.text
;
Description of the relative alignment of the crystal cell axes to the
Cartesian orthogonal axes as applied in the transformation matrix
_atom_sites_Cartn_transform.matrix.
;
_name.category_id atom_sites_Cartn_transform
_name.object_id axes
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'a parallel to x; b in the plane of y & z'
save_
save__atom_sites_Cartn_transform.mat_11
_definition.id '_atom_sites_Cartn_transform.mat_11'
loop_
_alias.definition_id
'_atom_sites_Cartn_transform.mat_11'
'_atom_sites_Cartn_tran_matrix_11'
'_atom_sites.Cartn_transf_matrix[1][1]'
_name.category_id atom_sites_Cartn_transform
_name.object_id mat_11
loop_
_method.purpose
_method.expression
Evaluation
;
With l as cell_length
With a as cell_angle
With r as cell_reciprocal_angle
_atom_sites_Cartn_transform.mat_11 = l.a*Sind(a.beta)*Sind(r.gamma)
;
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform fractional coordinates in the ATOM_SITE
category to Cartesian coordinates. The axial alignments of this
transformation are described in _atom_sites_Cartn_transform.axes.
The 3x1 translation is defined in _atom_sites_Cartn_transform.vector.
x' |11 12 13| x | 1 |
( y' )Cartesian = mat|21 22 23| * ( y )fractional + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code reciprocal_angstroms
save_
save__atom_sites_Cartn_transform.mat_12
_definition.id '_atom_sites_Cartn_transform.mat_12'
loop_
_alias.definition_id
'_atom_sites_Cartn_transform.mat_12'
'_atom_sites_Cartn_tran_matrix_12'
'_atom_sites.Cartn_transf_matrix[1][2]'
_name.category_id atom_sites_Cartn_transform
_name.object_id mat_12
loop_
_method.purpose
_method.expression
Evaluation
;
_atom_sites_Cartn_transform.mat_12 = 0.
;
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform fractional coordinates in the ATOM_SITE
category to Cartesian coordinates. The axial alignments of this
transformation are described in _atom_sites_Cartn_transform.axes.
The 3x1 translation is defined in _atom_sites_Cartn_transform.vector.
x' |11 12 13| x | 1 |
( y' )Cartesian = mat|21 22 23| * ( y )fractional + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code reciprocal_angstroms
save_
save__atom_sites_Cartn_transform.mat_13
_definition.id '_atom_sites_Cartn_transform.mat_13'
loop_
_alias.definition_id
'_atom_sites_Cartn_transform.mat_13'
'_atom_sites_Cartn_tran_matrix_13'
'_atom_sites.Cartn_transf_matrix[1][3]'
_name.category_id atom_sites_Cartn_transform
_name.object_id mat_13
loop_
_method.purpose
_method.expression
Evaluation
;
_atom_sites_Cartn_transform.mat_13 = 0.
;
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform fractional coordinates in the ATOM_SITE
category to Cartesian coordinates. The axial alignments of this
transformation are described in _atom_sites_Cartn_transform.axes.
The 3x1 translation is defined in _atom_sites_Cartn_transform.vector.
x' |11 12 13| x | 1 |
( y' )Cartesian = mat|21 22 23| * ( y )fractional + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code reciprocal_angstroms
save_
save__atom_sites_Cartn_transform.mat_21
_definition.id '_atom_sites_Cartn_transform.mat_21'
loop_
_alias.definition_id
'_atom_sites_Cartn_transform.mat_21'
'_atom_sites_Cartn_tran_matrix_21'
'_atom_sites.Cartn_transf_matrix[2][1]'
_name.category_id atom_sites_Cartn_transform
_name.object_id mat_21
loop_
_method.purpose
_method.expression
Evaluation
;
With l as cell_length
With a as cell_angle
With r as cell_reciprocal_angle
_atom_sites_Cartn_transform.mat_21 = -l.a*Sind(a.beta)*Cosd(r.gamma)
;
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform fractional coordinates in the ATOM_SITE
category to Cartesian coordinates. The axial alignments of this
transformation are described in _atom_sites_Cartn_transform.axes.
The 3x1 translation is defined in _atom_sites_Cartn_transform.vector.
x' |11 12 13| x | 1 |
( y' )Cartesian = mat|21 22 23| * ( y )fractional + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code reciprocal_angstroms
save_
save__atom_sites_Cartn_transform.mat_22
_definition.id '_atom_sites_Cartn_transform.mat_22'
loop_
_alias.definition_id
'_atom_sites_Cartn_transform.mat_22'
'_atom_sites_Cartn_tran_matrix_22'
'_atom_sites.Cartn_transf_matrix[2][2]'
_name.category_id atom_sites_Cartn_transform
_name.object_id mat_22
loop_
_method.purpose
_method.expression
Evaluation
;
With a as cell_angle
_atom_sites_Cartn_transform.mat_22 = _cell_length.b * Sind(a.alpha)
;
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform fractional coordinates in the ATOM_SITE
category to Cartesian coordinates. The axial alignments of this
transformation are described in _atom_sites_Cartn_transform.axes.
The 3x1 translation is defined in _atom_sites_Cartn_transform.vector.
x' |11 12 13| x | 1 |
( y' )Cartesian = mat|21 22 23| * ( y )fractional + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code reciprocal_angstroms
save_
save__atom_sites_Cartn_transform.mat_23
_definition.id '_atom_sites_Cartn_transform.mat_23'
loop_
_alias.definition_id
'_atom_sites_Cartn_transform.mat_23'
'_atom_sites_Cartn_tran_matrix_23'
'_atom_sites.Cartn_transf_matrix[2][3]'
_name.category_id atom_sites_Cartn_transform
_name.object_id mat_23
loop_
_method.purpose
_method.expression
Evaluation
;
_atom_sites_Cartn_transform.mat_23 = 0.
;
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform fractional coordinates in the ATOM_SITE
category to Cartesian coordinates. The axial alignments of this
transformation are described in _atom_sites_Cartn_transform.axes.
The 3x1 translation is defined in _atom_sites_Cartn_transform.vector.
x' |11 12 13| x | 1 |
( y' )Cartesian = mat|21 22 23| * ( y )fractional + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code reciprocal_angstroms
save_
save__atom_sites_Cartn_transform.mat_31
_definition.id '_atom_sites_Cartn_transform.mat_31'
loop_
_alias.definition_id
'_atom_sites_Cartn_transform.mat_31'
'_atom_sites_Cartn_tran_matrix_31'
'_atom_sites.Cartn_transf_matrix[3][1]'
_name.category_id atom_sites_Cartn_transform
_name.object_id mat_31
loop_
_method.purpose
_method.expression
Evaluation
;
With a as cell_angle
_atom_sites_Cartn_transform.mat_31 = _cell_length.a * Cosd(a.beta)
;
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform fractional coordinates in the ATOM_SITE
category to Cartesian coordinates. The axial alignments of this
transformation are described in _atom_sites_Cartn_transform.axes.
The 3x1 translation is defined in _atom_sites_Cartn_transform.vector.
x' |11 12 13| x | 1 |
( y' )Cartesian = mat|21 22 23| * ( y )fractional + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code reciprocal_angstroms
save_
save__atom_sites_Cartn_transform.mat_32
_definition.id '_atom_sites_Cartn_transform.mat_32'
loop_
_alias.definition_id
'_atom_sites_Cartn_transform.mat_32'
'_atom_sites_Cartn_tran_matrix_32'
'_atom_sites.Cartn_transf_matrix[3][2]'
_name.category_id atom_sites_Cartn_transform
_name.object_id mat_32
loop_
_method.purpose
_method.expression
Evaluation
;
With a as cell_angle
_atom_sites_Cartn_transform.mat_32 = _cell_length.b * Cosd(a.alpha)
;
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform fractional coordinates in the ATOM_SITE
category to Cartesian coordinates. The axial alignments of this
transformation are described in _atom_sites_Cartn_transform.axes.
The 3x1 translation is defined in _atom_sites_Cartn_transform.vector.
x' |11 12 13| x | 1 |
( y' )Cartesian = mat|21 22 23| * ( y )fractional + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code reciprocal_angstroms
save_
save__atom_sites_Cartn_transform.mat_33
_definition.id '_atom_sites_Cartn_transform.mat_33'
loop_
_alias.definition_id
'_atom_sites_Cartn_transform.mat_33'
'_atom_sites_Cartn_tran_matrix_33'
'_atom_sites.Cartn_transf_matrix[3][3]'
_name.category_id atom_sites_Cartn_transform
_name.object_id mat_33
loop_
_method.purpose
_method.expression
Evaluation
;
_atom_sites_Cartn_transform.mat_33 = _cell_length.c
;
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform fractional coordinates in the ATOM_SITE
category to Cartesian coordinates. The axial alignments of this
transformation are described in _atom_sites_Cartn_transform.axes.
The 3x1 translation is defined in _atom_sites_Cartn_transform.vector.
x' |11 12 13| x | 1 |
( y' )Cartesian = mat|21 22 23| * ( y )fractional + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code reciprocal_angstroms
save_
save__atom_sites_Cartn_transform.matrix
_definition.id '_atom_sites_Cartn_transform.matrix'
loop_
_alias.definition_id
'_atom_sites_Cartn_transform.matrix'
_definition.update 2012-12-11
_description.text
;
Matrix used to transform fractional coordinates in the ATOM_SITE
category to Cartesian coordinates. The axial alignments of this
transformation are described in _atom_sites_Cartn_transform.axes.
The 3 x 1 translation is defined in _atom_sites_Cartn_transform.vector.
x' |11 12 13| x | 1 |
( y' ) Cartesian = |21 22 23| * ( y ) fractional + v| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_name.category_id atom_sites_Cartn_transform
_name.object_id matrix
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3 3]
loop_
_method.purpose
_method.expression
Evaluation
;
With a as atom_sites_Cartn_transform
_atom_sites_Cartn_transform.matrix = [[a.mat_11, a.mat_12, a.mat_13],
[a.mat_21, a.mat_22, a.mat_23],
[a.mat_31, a.mat_32, a.mat_33]]
;
save_
save__atom_sites_Cartn_transform.vec_1
_definition.id '_atom_sites_Cartn_transform.vec_1'
loop_
_alias.definition_id
'_atom_sites_Cartn_transform.vec_1'
'_atom_sites_Cartn_tran_vector_1'
'_atom_sites.Cartn_transf_vector[1]'
_name.category_id atom_sites_Cartn_transform
_name.object_id vec_1
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform fractional coordinates in the ATOM_SITE
category to Cartesian coordinates. The axial alignments of this
transformation are described in _atom_sites_Cartn_transform.axes.
The 3x1 translation is defined in _atom_sites_Cartn_transform.vector.
x' |11 12 13| x | 1 |
( y' )Cartesian = mat|21 22 23| * ( y )fractional + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code reciprocal_angstroms
save_
save__atom_sites_Cartn_transform.vec_2
_definition.id '_atom_sites_Cartn_transform.vec_2'
loop_
_alias.definition_id
'_atom_sites_Cartn_transform.vec_2'
'_atom_sites_Cartn_tran_vector_2'
'_atom_sites.Cartn_transf_vector[2]'
_name.category_id atom_sites_Cartn_transform
_name.object_id vec_2
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform fractional coordinates in the ATOM_SITE
category to Cartesian coordinates. The axial alignments of this
transformation are described in _atom_sites_Cartn_transform.axes.
The 3x1 translation is defined in _atom_sites_Cartn_transform.vector.
x' |11 12 13| x | 1 |
( y' )Cartesian = mat|21 22 23| * ( y )fractional + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code reciprocal_angstroms
save_
save__atom_sites_Cartn_transform.vec_3
_definition.id '_atom_sites_Cartn_transform.vec_3'
loop_
_alias.definition_id
'_atom_sites_Cartn_transform.vec_3'
'_atom_sites_Cartn_tran_vector_3'
'_atom_sites.Cartn_transf_vector[3]'
_name.category_id atom_sites_Cartn_transform
_name.object_id vec_3
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform fractional coordinates in the ATOM_SITE
category to Cartesian coordinates. The axial alignments of this
transformation are described in _atom_sites_Cartn_transform.axes.
The 3x1 translation is defined in _atom_sites_Cartn_transform.vector.
x' |11 12 13| x | 1 |
( y' )Cartesian = mat|21 22 23| * ( y )fractional + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code reciprocal_angstroms
save_
save__atom_sites_Cartn_transform.vector
_definition.id '_atom_sites_Cartn_transform.vector'
loop_
_alias.definition_id
'_atom_sites_Cartn_transform.vector'
_definition.update 2012-11-20
_description.text
;
The 3x1 translation is used with _atom_sites_Cartn_transform.matrix
used to transform fractional coordinates to Cartesian coordinates.
The axial alignments of this transformation are described in
_atom_sites_Cartn_transform.axes.
;
_name.category_id atom_sites_Cartn_transform
_name.object_id vector
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With t as atom_sites_Cartn_transform
_atom_sites_Cartn_transform.vector = [ t.vec_1, t.vec_2, t.vec_3 ]
;
save_
save_ATOM_SITES_FRACT_TRANSFORM
_definition.id ATOM_SITES_FRACT_TRANSFORM
_definition.scope Category
_definition.class Set
_definition.update 2012-12-11
_description.text
;
The CATEGORY of data items used to describe the matrix elements
used to transform Cartesion coordinates into fractional coordinates
of all atom sites in a crystal structure.
;
_name.category_id ATOM_SITES
_name.object_id ATOM_SITES_FRACT_TRANSFORM
save_
save__atom_sites_fract_transform.axes
_definition.id '_atom_sites_fract_transform.axes'
loop_
_alias.definition_id
'_atom_sites_fract_transform.axes'
'_atom_sites_fract_transform_axes'
'_atom_sites.fract_transform_axes'
_definition.update 2012-12-11
_description.text
;
Description of the relative alignment of the crystal cell axes to the
Cartesian orthogonal axes as applied in the transformation matrix
_atom_sites_fract_transform.matrix.
;
_name.category_id atom_sites_fract_transform
_name.object_id axes
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'a parallel to x; b in the plane of y & z'
save_
save__atom_sites_fract_transform.mat_11
_definition.id '_atom_sites_fract_transform.mat_11'
loop_
_alias.definition_id
'_atom_sites_fract_transform.mat_11'
'_atom_sites_fract_tran_matrix_11'
'_atom_sites.fract_transf_matrix[1][1]'
_name.category_id atom_sites_fract_transform
_name.object_id mat_11
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform Cartesian coordinates in the ATOM_SITE
category to fractional coordinates. The axial alignments of this
transformation are described in _atom_sites_fract_transform.axes.
The 3x1 translation is defined in _atom_sites_fract_transform.vector.
x' |11 12 13| x | 1 |
( y' )fractional = mat|21 22 23| * ( y )Cartesian + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code none
save_
save__atom_sites_fract_transform.mat_12
_definition.id '_atom_sites_fract_transform.mat_12'
loop_
_alias.definition_id
'_atom_sites_fract_transform.mat_12'
'_atom_sites_fract_tran_matrix_12'
'_atom_sites.fract_transf_matrix[1][2]'
_name.category_id atom_sites_fract_transform
_name.object_id mat_12
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform Cartesian coordinates in the ATOM_SITE
category to fractional coordinates. The axial alignments of this
transformation are described in _atom_sites_fract_transform.axes.
The 3x1 translation is defined in _atom_sites_fract_transform.vector.
x' |11 12 13| x | 1 |
( y' )fractional = mat|21 22 23| * ( y )Cartesian + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code none
save_
save__atom_sites_fract_transform.mat_13
_definition.id '_atom_sites_fract_transform.mat_13'
loop_
_alias.definition_id
'_atom_sites_fract_transform.mat_13'
'_atom_sites_fract_tran_matrix_13'
'_atom_sites.fract_transf_matrix[1][3]'
_name.category_id atom_sites_fract_transform
_name.object_id mat_13
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform Cartesian coordinates in the ATOM_SITE
category to fractional coordinates. The axial alignments of this
transformation are described in _atom_sites_fract_transform.axes.
The 3x1 translation is defined in _atom_sites_fract_transform.vector.
x' |11 12 13| x | 1 |
( y' )fractional = mat|21 22 23| * ( y )Cartesian + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code none
save_
save__atom_sites_fract_transform.mat_21
_definition.id '_atom_sites_fract_transform.mat_21'
loop_
_alias.definition_id
'_atom_sites_fract_transform.mat_21'
'_atom_sites_fract_tran_matrix_21'
'_atom_sites.fract_transf_matrix[2][1]'
_name.category_id atom_sites_fract_transform
_name.object_id mat_21
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform Cartesian coordinates in the ATOM_SITE
category to fractional coordinates. The axial alignments of this
transformation are described in _atom_sites_fract_transform.axes.
The 3x1 translation is defined in _atom_sites_fract_transform.vector.
x' |11 12 13| x | 1 |
( y' )fractional = mat|21 22 23| * ( y )Cartesian + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code none
save_
save__atom_sites_fract_transform.mat_22
_definition.id '_atom_sites_fract_transform.mat_22'
loop_
_alias.definition_id
'_atom_sites_fract_transform.mat_22'
'_atom_sites_fract_tran_matrix_22'
'_atom_sites.fract_transf_matrix[2][2]'
_name.category_id atom_sites_fract_transform
_name.object_id mat_22
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform Cartesian coordinates in the ATOM_SITE
category to fractional coordinates. The axial alignments of this
transformation are described in _atom_sites_fract_transform.axes.
The 3x1 translation is defined in _atom_sites_fract_transform.vector.
x' |11 12 13| x | 1 |
( y' )fractional = mat|21 22 23| * ( y )Cartesian + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code none
save_
save__atom_sites_fract_transform.mat_23
_definition.id '_atom_sites_fract_transform.mat_23'
loop_
_alias.definition_id
'_atom_sites_fract_transform.mat_23'
'_atom_sites_fract_tran_matrix_23'
'_atom_sites.fract_transf_matrix[2][3]'
_name.category_id atom_sites_fract_transform
_name.object_id mat_23
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform Cartesian coordinates in the ATOM_SITE
category to fractional coordinates. The axial alignments of this
transformation are described in _atom_sites_fract_transform.axes.
The 3x1 translation is defined in _atom_sites_fract_transform.vector.
x' |11 12 13| x | 1 |
( y' )fractional = mat|21 22 23| * ( y )Cartesian + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code none
save_
save__atom_sites_fract_transform.mat_31
_definition.id '_atom_sites_fract_transform.mat_31'
loop_
_alias.definition_id
'_atom_sites_fract_transform.mat_31'
'_atom_sites_fract_tran_matrix_31'
'_atom_sites.fract_transf_matrix[3][1]'
_name.category_id atom_sites_fract_transform
_name.object_id mat_31
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform Cartesian coordinates in the ATOM_SITE
category to fractional coordinates. The axial alignments of this
transformation are described in _atom_sites_fract_transform.axes.
The 3x1 translation is defined in _atom_sites_fract_transform.vector.
x' |11 12 13| x | 1 |
( y' )fractional = mat|21 22 23| * ( y )Cartesian + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code none
save_
save__atom_sites_fract_transform.mat_32
_definition.id '_atom_sites_fract_transform.mat_32'
loop_
_alias.definition_id
'_atom_sites_fract_transform.mat_32'
'_atom_sites_fract_tran_matrix_32'
'_atom_sites.fract_transf_matrix[3][2]'
_name.category_id atom_sites_fract_transform
_name.object_id mat_32
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform Cartesian coordinates in the ATOM_SITE
category to fractional coordinates. The axial alignments of this
transformation are described in _atom_sites_fract_transform.axes.
The 3x1 translation is defined in _atom_sites_fract_transform.vector.
x' |11 12 13| x | 1 |
( y' )fractional = mat|21 22 23| * ( y )Cartesian + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code none
save_
save__atom_sites_fract_transform.mat_33
_definition.id '_atom_sites_fract_transform.mat_33'
loop_
_alias.definition_id
'_atom_sites_fract_transform.mat_33'
'_atom_sites_fract_tran_matrix_33'
'_atom_sites.fract_transf_matrix[3][3]'
_name.category_id atom_sites_fract_transform
_name.object_id mat_33
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform Cartesian coordinates in the ATOM_SITE
category to fractional coordinates. The axial alignments of this
transformation are described in _atom_sites_fract_transform.axes.
The 3x1 translation is defined in _atom_sites_fract_transform.vector.
x' |11 12 13| x | 1 |
( y' )fractional = mat|21 22 23| * ( y )Cartesian + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code none
save_
save__atom_sites_fract_transform.matrix
_definition.id '_atom_sites_fract_transform.matrix'
loop_
_alias.definition_id
'_atom_sites_fract_transform.matrix'
_definition.update 2012-12-11
_description.text
;
Matrix used to transform fractional coordinates in the ATOM_SITE
category to Cartesian coordinates. The axial alignments of this
transformation are described in _atom_sites_fract_transform.axes.
The 3 x 1 translation is defined in _atom_sites_fract_transform.vector.
x' |11 12 13| x | 1 |
( y' )fractional = mat |21 22 23| * ( y ) Cartesian + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_name.category_id atom_sites_fract_transform
_name.object_id matrix
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3 3]
loop_
_method.purpose
_method.expression
Evaluation
;
With a as atom_sites_fract_transform
_atom_sites_fract_transform.matrix = [[a.mat_11, a.mat_12, a.mat_13],
[a.mat_21, a.mat_22, a.mat_23],
[a.mat_31, a.mat_32, a.mat_33]]
;
save_
save__atom_sites_fract_transform.vec_1
_definition.id '_atom_sites_fract_transform.vec_1'
loop_
_alias.definition_id
'_atom_sites_fract_transform.vec_1'
'_atom_sites_fract_tran_vector_1'
'_atom_sites.fract_transf_vector[1]'
_name.category_id atom_sites_fract_transform
_name.object_id vec_1
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform Cartesian coordinates in the ATOM_SITE
category to fractional coordinates. The axial alignments of this
transformation are described in _atom_sites_fract_transform.axes.
The 3x1 translation is defined in _atom_sites_fract_transform.vector.
x' |11 12 13| x | 1 |
( y' )fractional = mat|21 22 23| * ( y )Cartesian + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code none
save_
save__atom_sites_fract_transform.vec_2
_definition.id '_atom_sites_fract_transform.vec_2'
loop_
_alias.definition_id
'_atom_sites_fract_transform.vec_2'
'_atom_sites_fract_tran_vector_2'
'_atom_sites.fract_transf_vector[2]'
_name.category_id atom_sites_fract_transform
_name.object_id vec_2
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform Cartesian coordinates in the ATOM_SITE
category to fractional coordinates. The axial alignments of this
transformation are described in _atom_sites_fract_transform.axes.
The 3x1 translation is defined in _atom_sites_fract_transform.vector.
x' |11 12 13| x | 1 |
( y' )fractional = mat|21 22 23| * ( y )Cartesian + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code none
save_
save__atom_sites_fract_transform.vec_3
_definition.id '_atom_sites_fract_transform.vec_3'
loop_
_alias.definition_id
'_atom_sites_fract_transform.vec_3'
'_atom_sites_fract_tran_vector_3'
'_atom_sites.fract_transf_vector[3]'
_name.category_id atom_sites_fract_transform
_name.object_id vec_3
_type.contents Real
_type.purpose Measurand
_description.text
;
Matrix used to transform Cartesian coordinates in the ATOM_SITE
category to fractional coordinates. The axial alignments of this
transformation are described in _atom_sites_fract_transform.axes.
The 3x1 translation is defined in _atom_sites_fract_transform.vector.
x' |11 12 13| x | 1 |
( y' )fractional = mat|21 22 23| * ( y )Cartesian + vec| 2 |
z' |31 32 33| z | 3 |
The default transformation matrix uses Rollet's axial
assignments with cell vectors a,b,c aligned with orthogonal
axes X,Y,Z so that c||Z and b in plane YZ.
;
_enumeration.default ?
_type.source Derived
_type.container Single
_definition.update 2012-12-11
_units.code none
save_
save__atom_sites_fract_transform.vector
_definition.id '_atom_sites_fract_transform.vector'
loop_
_alias.definition_id
'_atom_sites_fract_transform.vector'
_definition.update 2012-11-20
_description.text
;
The 3x1 translation is used with _atom_sites_fract_transform.matrix
used to transform Cartesian coordinates to fractional coordinates.
The axial alignments of this transformation are described in
_atom_sites_fract_transform.axes.
;
_name.category_id atom_sites_fract_transform
_name.object_id vector
_type.purpose Measurand
_type.source Derived
_type.container Matrix
_type.contents Real
_type.dimension [3]
loop_
_method.purpose
_method.expression
Evaluation
;
With t as atom_sites_fract_transform
_atom_sites_fract_transform.vector = [ t.vec_1, t.vec_2, t.vec_3 ]
;
save_
save_ATOM_TYPE
_definition.id ATOM_TYPE
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to describe atomic type information
used in crystallographic structure studies.
;
_name.category_id ATOM
_name.object_id ATOM_TYPE
_category.key_id '_atom_type.key'
_category.key_list ['_atom_type.symbol']
loop_
_method.purpose
_method.expression
Evaluation
;
typelist = List()
Loop a as atom_site {
type = AtomType ( a.label )
If( type not in typelist ) typelist ++= type
}
For type in typelist {
atom_type(.symbol = type )
}
;
save_
save__atom_type.analytical_mass_percent
_definition.id '_atom_type.analytical_mass_percent'
loop_
_alias.definition_id
'_atom_type.analytical_mass_percent'
'_atom_type_analytical_mass_%'
'_atom_type.analytical_mass_%'
_definition.update 2013-04-11
_description.text
;
Mass percentage of this atom type derived from chemical analysis.
;
_name.category_id atom_type
_name.object_id analytical_mass_percent
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:100.
_units.code none
save_
save__atom_type.atomic_mass
_definition.id '_atom_type.atomic_mass'
loop_
_alias.definition_id
'_atom_type.atomic_mass'
_definition.update 2012-11-20
_description.text
;
Mass of this atom type.
;
_name.category_id atom_type
_name.object_id atomic_mass
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.def_index_id '_atom_type.symbol'
_units.code dalton
loop_
_enumeration_default.index
_enumeration_default.value
H 1.008
D 2.008
H1- 1.008
He 4.003
Li 6.941
Li1+ 6.941
Be 9.012
Be2+ 9.012
B 10.811
C 12.011
N 14.007
O 15.999
O1- 15.999
F 18.998
F1- 18.998
Ne 20.179
Na 22.990
Na1+ 22.990
Mg 24.305
Mg2+ 24.305
Al 26.982
Al3+ 26.982
Si 28.086
Si4+ 28.086
P 30.974
S 32.066
Cl 35.453
Cl1- 35.453
Ar 39.948
K 39.098
K1+ 39.098
Ca 40.078
Ca2+ 40.078
Sc 44.956
Sc3+ 44.956
Ti 47.88
Ti2+ 47.88
Ti3+ 47.88
Ti4+ 47.88
V 50.942
V2+ 50.942
V3+ 50.942
V5+ 50.942
Cr 51.996
Cr2+ 51.996
Cr3+ 51.996
Mn 54.938
Mn2+ 54.938
Mn3+ 54.938
Mn4+ 54.938
Fe 55.847
Fe2+ 55.847
Fe3+ 55.847
Co 58.933
Co2+ 58.933
Co3+ 58.933
Ni 58.69
Ni2+ 58.69
Ni3+ 58.69
Cu 63.546
Cu1+ 63.546
Cu2+ 63.546
Zn 65.39
Zn2+ 65.39
Ga 69.723
Ga3+ 69.723
Ge 72.59
Ge4+ 72.59
As 74.922
Se 78.96
Br 79.904
Br1- 79.904
Kr 83.80
Rb 85.468
Rb1+ 85.468
Sr 87.62
Sr2+ 87.62
Y 88.906
Y3+ 88.906
Zr 91.224
Zr4+ 91.224
Nb 92.906
Nb3+ 92.906
Nb5+ 92.906
Mo 95.94
Mo3+ 95.94
Mo5+ 95.94
Mo6+ 95.94
Tc 98.906
Ru 101.07
Ru3+ 101.07
Ru4+ 101.07
Rh 102.906
Rh3+ 102.906
Rh4+ 102.906
Pd 106.42
Pd2+ 106.42
Pd4+ 106.42
Ag 107.868
Ag1+ 107.868
Ag2+ 107.868
Cd 112.41
Cd2+ 112.41
In 114.82
In3+ 114.82
Sn 118.71
Sn2+ 118.71
Sn4+ 118.71
Sb 121.75
Sb3+ 121.75
Sb5+ 121.75
Te 127.60
I 126.905
I1- 126.905
Xe 131.29
Cs 132.905
Cs1+ 132.905
Ba 137.33
Ba2+ 137.33
La 138.906
La3+ 138.906
Ce 140.12
Ce3+ 140.12
Ce4+ 140.12
Pr 140.908
Pr3+ 140.908
Pr4+ 140.908
Nd 144.24
Nd3+ 144.24
Pm 147.
Sm 150.36
Sm3+ 150.36
Eu 151.96
Eu2+ 151.96
Eu3+ 151.96
Gd 157.25
Gd3+ 157.25
Tb 158.926
Tb3+ 158.926
Dy 162.5
Dy3+ 162.5
Ho 164.93
Ho3+ 164.93
Er 167.26
Er3+ 167.26
Tm 168.934
Tm3+ 168.934
Yb 173.04
Yb2+ 173.04
Yb3+ 173.04
Lu 174.967
Lu3+ 174.967
Hf 178.49
Hf4+ 178.49
Ta 180.948
Ta5+ 180.948
W 183.85
W6+ 183.85
Re 186.207
Os 190.2
Os4+ 190.2
Ir 192.22
Ir3+ 192.22
Ir4+ 192.22
Pt 195.08
Pt2+ 195.08
Pt4+ 195.08
Au 196.966
Au1+ 196.966
Au3+ 196.966
Hg 200.59
Hg1+ 200.59
Hg2+ 200.59
Tl 204.383
TL1+ 204.383
Tl3+ 204.383
Pb 207.2
Pb2+ 207.2
Pb4+ 207.2
Bi 208.980
Bi3+ 208.980
Bi5+ 208.980
Po 209.
At 210.
Rn 222.
Fr 223.
Ra 226.025
Ra2+ 226.025
Ac 227.
Ac3+ 227.
Th 232.038
Th4+ 232.038
Pa 231.036
U 238.029
U3+ 238.029
U4+ 238.029
U6+ 238.029
Np 237.048
Np3+ 237.048
Np4+ 237.048
Np6+ 237.048
Pu 242.
Pu3+ 242.
Pu4+ 242.
Pu6+ 242.
Am 243.
Cm 247.
Bk 247.
Cf 249.
save_
save__atom_type.atomic_number
_definition.id '_atom_type.atomic_number'
loop_
_alias.definition_id
'_atom_type.atomic_number'
_definition.update 2012-11-20
_description.text
;
Atomic number of this atom type.
;
_name.category_id atom_type
_name.object_id atomic_number
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Index
_enumeration.def_index_id '_atom_type.symbol'
loop_
_enumeration_default.index
_enumeration_default.value
H 01
D 01
H1- 01
He 02
Li 03
Li1+ 03
Be 04
Be2+ 04
B 05
C 06
N 07
O 08
O1- 08
F 09
F1- 09
Ne 10
Na 11
Na1+ 11
Mg 12
Mg2+ 12
Al 13
Al3+ 13
Si 14
Si4+ 14
P 15
S 16
Cl 17
Cl1- 17
Ar 18
K 19
K1+ 19
Ca 20
Ca2+ 20
Sc 21
Sc3+ 21
Ti 22
Ti2+ 22
Ti3+ 22
Ti4+ 22
V 23
V2+ 23
V3+ 23
V5+ 23
Cr 24
Cr2+ 24
Cr3+ 24
Mn 25
Mn2+ 25
Mn3+ 25
Mn4+ 25
Fe 26
Fe2+ 26
Fe3+ 26
Co 27
Co2+ 27
Co3+ 27
Ni 28
Ni2+ 28
Ni3+ 28
Cu 29
Cu1+ 29
Cu2+ 29
Zn 30
Zn2+ 30
Ga 31
Ga3+ 31
Ge 32
Ge4+ 32
As 33
Se 34
Br 35
Br1- 35
Kr 36
Rb 37
Rb1+ 37
Sr 38
Sr2+ 38
Y 39
Y3+ 39
Zr 40
Zr4+ 40
Nb 41
Nb3+ 41
Nb5+ 41
Mo 42
Mo3+ 42
Mo5+ 42
Mo6+ 42
Tc 43
Ru 44
Ru3+ 44
Ru4+ 44
Rh 45
Rh3+ 45
Rh4+ 45
Pd 46
Pd2+ 46
Pd4+ 46
Ag 47
Ag1+ 47
Ag2+ 47
Cd 48
Cd2+ 48
In 49
In3+ 49
Sn 50
Sn2+ 50
Sn4+ 50
Sb 51
Sb3+ 51
Sb5+ 51
Te 52
I 53
I1- 53
Xe 54
Cs 55
Cs1+ 55
Ba 56
Ba2+ 56
La 57
La3+ 57
Ce 58
Ce3+ 58
Ce4+ 58
Pr 59
Pr3+ 59
Pr4+ 59
Nd 60
Nd3+ 60
Pm 61
Sm 62
Sm3+ 62
Eu 63
Eu2+ 63
Eu3+ 63
Gd 64
Gd3+ 64
Tb 65
Tb3+ 65
Dy 66
Dy3+ 66
Ho 67
Ho3+ 67
Er 68
Er3+ 68
Tm 69
Tm3+ 69
Yb 70
Yb2+ 70
Yb3+ 70
Lu 71
Lu3+ 71
Hf 72
Hf4+ 72
Ta 73
Ta5+ 73
W 74
W6+ 74
Re 75
Os 76
Os4+ 76
Ir 77
Ir3+ 77
Ir4+ 77
Pt 78
Pt2+ 78
Pt4+ 78
Au 79
Au1+ 79
Au3+ 79
Hg 80
Hg1+ 80
Hg2+ 80
Tl 81
TL1+ 81
Tl3+ 81
Pb 82
Pb2+ 82
Pb4+ 82
Bi 83
Bi3+ 83
Bi5+ 83
Po 84
At 85
Rn 86
Fr 87
Ra 88
Ra2+ 88
Ac 89
Ac3+ 89
Th 90
Th4+ 90
Pa 91
U 92
U3+ 92
U4+ 92
U6+ 92
Np 93
Np3+ 93
Np4+ 93
Np6+ 93
Pu 94
Pu3+ 94
Pu4+ 94
Pu6+ 94
Am 95
Cm 96
Bk 97
Cf 98
save_
save__atom_type.description
_definition.id '_atom_type.description'
loop_
_alias.definition_id
'_atom_type.description'
'_atom_type_description'
_definition.update 2012-11-20
_description.text
;
A description of the atom(s) designated by this atom type. In
most cases this will be the element name and oxidation state of
a single atom species. For disordered or nonstoichiometric
structures it will describe a combination of atom species.
;
_name.category_id atom_type
_name.object_id description
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
deuterium
0.34Fe+0.66Ni
save_
save__atom_type.display_colour
_definition.id '_atom_type.display_colour'
loop_
_alias.definition_id
'_atom_type.display_colour'
_definition.update 2012-11-20
_description.text
;
The display colour assigned to this atom type. Note that the
possible colours are enumerated in the display_colour list
category of items.
;
_name.category_id atom_type
_name.object_id display_colour
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
_enumeration.def_index_id '_atom_type.symbol'
loop_
_enumeration_set.state
_enumeration_set.detail
black '[ 000, 000, 000 ]'
white '[ 255, 255, 255 ]'
grey '[ 192, 192, 192 ]'
grey_light '[ 211, 211, 211 ]'
grey_slate '[ 112, 128, 144 ]'
blue '[ 000, 000, 255 ]'
blue_light '[ 176, 224, 230 ]'
blue_medium '[ 000, 000, 205 ]'
blue_dark '[ 025, 025, 112 ]'
blue_navy '[ 000, 000, 128 ]'
blue_royal '[ 065, 105, 225 ]'
blue_sky '[ 135, 206, 235 ]'
blue_steel '[ 070, 130, 180 ]'
turquoise '[ 064, 224, 208 ]'
cyan '[ 000, 255, 255 ]'
cyan_light '[ 224, 255, 255 ]'
green '[ 000, 255, 000 ]'
green_light '[ 152, 251, 152 ]'
green_dark '[ 000, 100, 000 ]'
green_sea '[ 046, 139, 087 ]'
green_lime '[ 050, 205, 050 ]'
green_olive '[ 107, 142, 035 ]'
green_khaki '[ 240, 230, 140 ]'
yellow '[ 255, 255, 000 ]'
yellow_light '[ 255, 255, 224 ]'
yellow_gold '[ 255, 215, 000 ]'
brown '[ 165, 042, 042 ]'
brown_sienna '[ 160, 082, 045 ]'
brown_beige '[ 245, 245, 220 ]'
brown_tan '[ 210, 180, 140 ]'
salmon '[ 250, 128, 114 ]'
salmon_light '[ 255, 160, 122 ]'
salmon_dark '[ 233, 150, 122 ]'
orange '[ 255, 165, 000 ]'
orange_dark '[ 255, 140, 000 ]'
red '[ 255, 000, 000 ]'
red_coral '[ 255, 127, 080 ]'
red_tomato '[ 255, 099, 071 ]'
red_orange '[ 255, 069, 000 ]'
red_violet '[ 219, 112, 147 ]'
red_maroon '[ 176, 048, 096 ]'
pink '[ 255, 192, 203 ]'
pink_light '[ 255, 182, 193 ]'
pink_deep '[ 255, 020, 147 ]'
pink_hot '[ 255, 105, 180 ]'
violet '[ 238, 130, 238 ]'
violet_red '[ 208, 032, 144 ]'
violet_magenta '[ 255, 000, 255 ]'
violet_dark '[ 148, 000, 211 ]'
violet_blue '[ 138, 043, 226 ]'
loop_
_enumeration_default.index
_enumeration_default.value
H white
D blue_light
H1- white
He unknown
Li unknown
Li1+ unknown
Be unknown
Be2+ unknown
B unknown
C steel_grey
N blue
O red
O1- red
F green
F1- green
Ne unknown
Na magenta
Na1+ magenta
Mg magenta
Mg2+ magenta
Al magenta
Al3+ magenta
Si unknown
Si4+ unknown
P magenta
S yellow
Cl green
Cl1- green
Ar unknown
K magenta
K1+ magenta
Ca magenta
Ca2+ magenta
Sc unknown
Sc3+ unknown
Ti magenta
Ti2+ magenta
Ti3+ magenta
Ti4+ magenta
V magenta
V2+ magenta
V3+ magenta
V5+ magenta
Cr magenta
Cr2+ magenta
Cr3+ magenta
Mn magenta
Mn2+ magenta
Mn3+ magenta
Mn4+ magenta
Fe magenta
Fe2+ magenta
Fe3+ magenta
Co magenta
Co2+ magenta
Co3+ magenta
Ni magenta
Ni2+ magenta
Ni3+ magenta
Cu magenta
Cu1+ magenta
Cu2+ magenta
Zn magenta
Zn2+ magenta
Ga magenta
Ga3+ magenta
Ge magenta
Ge4+ magenta
As magenta
Se yellow
Br green
Br1- green
Kr unknown
Rb unknown
Rb1+ unknown
Sr unknown
Sr2+ unknown
Y unknown
Y3+ unknown
Zr unknown
Zr4+ unknown
Nb unknown
Nb3+ unknown
Nb5+ unknown
Mo unknown
Mo3+ magenta
Mo5+ magenta
Mo6+ magenta
Tc unknown
Ru unknown
Ru3+ unknown
Ru4+ unknown
Rh unknown
Rh3+ unknown
Rh4+ unknown
Pd unknown
Pd2+ unknown
Pd4+ unknown
Ag magenta
Ag1+ magenta
Ag2+ magenta
Cd magenta
Cd2+ magenta
In unknown
In3+ unknown
Sn magenta
Sn2+ magenta
Sn4+ magenta
Sb magenta
Sb3+ magenta
Sb5+ magenta
Te unknown
I green
I1- green
Xe unknown
Cs unknown
Cs1+ unknown
Ba unknown
Ba2+ unknown
La unknown
La3+ unknown
Ce unknown
Ce3+ unknown
Ce4+ unknown
Pr unknown
Pr3+ unknown
Pr4+ unknown
Nd unknown
Nd3+ unknown
Pm unknown
Sm unknown
Sm3+ unknown
Eu unknown
Eu2+ unknown
Eu3+ unknown
Gd unknown
Gd3+ unknown
Tb unknown
Tb3+ unknown
Dy unknown
Dy3+ unknown
Ho unknown
Ho3+ unknown
Er unknown
Er3+ unknown
Tm unknown
Tm3+ unknown
Yb unknown
Yb2+ unknown
Yb3+ unknown
Lu unknown
Lu3+ unknown
Hf unknown
Hf4+ unknown
Ta unknown
Ta5+ unknown
W unknown
W6+ unknown
Re unknown
Os unknown
Os4+ unknown
Ir unknown
Ir3+ unknown
Ir4+ unknown
Pt magenta
Pt2+ magenta
Pt4+ magenta
Au magenta
Au1+ magenta
Au3+ magenta
Hg magenta
Hg1+ magenta
Hg2+ magenta
Tl unknown
TL1+ unknown
Tl3+ unknown
Pb magenta
Pb2+ magenta
Pb4+ magenta
Bi magenta
Bi3+ magenta
Bi5+ magenta
Po unknown
At unknown
Rn unknown
Fr unknown
Ra unknown
Ra2+ unknown
Ac unknown
Ac3+ unknown
Th unknown
Th4+ unknown
Pa unknown
U unknown
U3+ unknown
U4+ unknown
U6+ unknown
Np unknown
Np3+ unknown
Np4+ unknown
Np6+ unknown
Pu unknown
Pu3+ unknown
Pu4+ unknown
Pu6+ unknown
Am unknown
Cm unknown
Bk unknown
Cf unknown
save_
save__atom_type.electron_count
_definition.id '_atom_type.electron_count'
loop_
_alias.definition_id
'_atom_type.electron_count'
_definition.update 2012-11-20
_description.text
;
Number of electrons in this atom type.
;
_name.category_id atom_type
_name.object_id electron_count
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Index
_enumeration.def_index_id '_atom_type.symbol'
_enumeration.range 1:
loop_
_enumeration_default.index
_enumeration_default.value
H 01
D 01
H1- 02
He 02
Li 03
Li1+ 02
Be 04
Be2+ 02
B 05
C 06
N 07
O 08
O1- 09
F 09
F1- 10
Ne 10
Na 11
Na1+ 10
Mg 12
Mg2+ 10
Al 13
Al3+ 10
Si 14
Si4+ 10
P 15
S 16
Cl 17
Cl1- 18
Ar 18
K 19
K1+ 18
Ca 20
Ca2+ 18
Sc 21
Sc3+ 18
Ti 22
Ti2+ 20
Ti3+ 19
Ti4+ 18
V 23
V2+ 21
V3+ 20
V5+ 18
Cr 24
Cr2+ 22
Cr3+ 21
Mn 25
Mn2+ 23
Mn3+ 22
Mn4+ 21
Fe 26
Fe2+ 24
Fe3+ 23
Co 27
Co2+ 25
Co3+ 24
Ni 28
Ni2+ 26
Ni3+ 25
Cu 29
Cu1+ 28
Cu2+ 27
Zn 30
Zn2+ 28
Ga 31
Ga3+ 28
Ge 32
Ge4+ 28
As 33
Se 34
Br 35
Br1- 36
Kr 36
Rb 37
Rb1+ 36
Sr 38
Sr2+ 36
Y 39
Y3+ 36
Zr 40
Zr4+ 36
Nb 41
Nb3+ 38
Nb5+ 36
Mo 42
Mo3+ 39
Mo5+ 37
Mo6+ 36
Tc 43
Ru 44
Ru3+ 41
Ru4+ 40
Rh 45
Rh3+ 42
Rh4+ 41
Pd 46
Pd2+ 44
Pd4+ 42
Ag 47
Ag1+ 46
Ag2+ 45
Cd 48
Cd2+ 46
In 49
In3+ 46
Sn 50
Sn2+ 48
Sn4+ 46
Sb 51
Sb3+ 48
Sb5+ 46
Te 52
I 53
I1- 54
Xe 54
Cs 55
Cs1+ 54
Ba 56
Ba2+ 54
La 57
La3+ 54
Ce 58
Ce3+ 55
Ce4+ 54
Pr 59
Pr3+ 56
Pr4+ 55
Nd 60
Nd3+ 57
Pm 61
Sm 62
Sm3+ 59
Eu 63
Eu2+ 61
Eu3+ 60
Gd 64
Gd3+ 61
Tb 65
Tb3+ 62
Dy 66
Dy3+ 63
Ho 67
Ho3+ 64
Er 68
Er3+ 65
Tm 69
Tm3+ 66
Yb 70
Yb2+ 68
Yb3+ 67
Lu 71
Lu3+ 68
Hf 72
Hf4+ 68
Ta 73
Ta5+ 68
W 74
W6+ 68
Re 75
Os 76
Os4+ 72
Ir 77
Ir3+ 74
Ir4+ 73
Pt 78
Pt2+ 76
Pt4+ 74
Au 79
Au1+ 78
Au3+ 76
Hg 80
Hg1+ 79
Hg2+ 78
Tl 81
TL1+ 80
Tl3+ 78
Pb 82
Pb2+ 80
Pb4+ 78
Bi 83
Bi3+ 80
Bi5+ 78
Po 84
At 85
Rn 86
Fr 87
Ra 88
Ra2+ 86
Ac 89
Ac3+ 86
Th 90
Th4+ 86
Pa 91
U 92
U3+ 89
U4+ 88
U6+ 84
Np 93
Np3+ 90
Np4+ 89
Np6+ 87
Pu 94
Pu3+ 91
Pu4+ 90
Pu6+ 88
Am 95
Cm 96
Bk 97
Cf 98
save_
save__atom_type.element_symbol
_definition.id '_atom_type.element_symbol'
loop_
_alias.definition_id
'_atom_type.element_symbol'
_definition.update 2012-11-20
_description.text
;
Element symbol for of this atom type. The default value is extracted
from the ion-to-element enumeration_default list using the index
value of atom_type.symbol.
;
_name.category_id atom_type
_name.object_id element_symbol
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
_enumeration.def_index_id '_atom_type.symbol'
loop_
_enumeration_set.state
_enumeration_set.detail
Ac Actinium
Ag Silver
Al Aluminum
Am Americium
Ar Argon
As Arsenic
At Astatine
Au Gold
B Boron
Ba Barium
Be Beryllium
Bh Bohrium
Bi Bismuth
Bk Berkelium
Br Bromine
C Carbon
Ca Calcium
Cd Cadmium
Ce Cerium
Cf Californium
Cl Chlorine
Cm Curium
Co Cobalt
Cr Chromium
Cs Cesium
Cu Copper
Db Dubnium
Ds Darmstadtium
Dy Dysprosium
Er Erbium
Es Einsteinium
Eu Europium
F Fluorine
Fe Iron
Fm Fermium
Fr Francium
Ga Gallium
Gd Gadolinium
Ge Germanium
H Hydrogen
He Helium
Hf Hafnium
Hg Mercury
Ho Holmium
Hs Hassium
I Iodine
In Indium
Ir Iridium
K Potassium
Kr Krypton
La Lanthanum
Li Lithium
Lr Lawrencium
Lu Lutetium
Md Mendelevium
Mg Magnesium
Mn Manganese
Mo Molybdenum
Mt Meitnerium
N Nitrogen
Na Sodium
Ne Neon
Nb Niobium
Nd Neodymium
Ni Nickel
No Nobelium
Np Neptunium
O Oxygen
Os Osmium
P Phosphorus
Pd Palladium
Po Polonium
Pb Lead
Pt Platinum
Pr Praseodymium
Pm Promethium
Pu Plutonium
Pa Protactinium
Ra Radium
Rb Rubidium
Re Rhenium
Rf Rutherfordium
Rh Rhodium
Rn Radon
Ru Ruthenium
S Sulfur
Sb Antimony
Sc Scandium
Se Selenium
Sg Seaborgium
Si Silicon
Sm Samarium
Sn Tin
Sr Strontium
Ta Tantalum
Tb Terbium
Tc Technetium
Te Tellurium
Th Thorium
Ti Titanium
Tl Thallium
Tm Thulium
U Uranium
Uub Ununbium
Uun Ununnilium
Uuu Ununumium
V Vanadium
W Tungsten
Xe Xenon
Y Yttrium
Yb Ytterbium
Zn Zinc
Zr Zirconium
loop_
_enumeration_default.index
_enumeration_default.value
H H
D D
H1- H
He He
Li Li
Li1+ Li
Be Be
Be2+ Be
B B
C C
N N
O O
O1- O
F F
F1- F
Ne Ne
Na Na
Na1+ Na
Mg Mg
Mg2+ Mg
Al Al
Al3+ Al
Si Si
Si4+ Si
P P
S S
Cl Cl
Cl1- Cl
Ar Ar
K K
K1+ K
Ca Ca
Ca2+ Ca
Sc Sc
Sc3+ Sc
Ti Ti
Ti2+ Ti
Ti3+ Ti
Ti4+ Ti
V V
V2+ V
V3+ V
V5+ V
Cr Cr
Cr2+ Cr
Cr3+ Cr
Mn Mn
Mn2+ Mn
Mn3+ Mn
Mn4+ Mn
Fe Fe
Fe2+ Fe
Fe3+ Fe
Co Co
Co2+ Co
Co3+ Co
Ni Ni
Ni2+ Ni
Ni3+ Ni
Cu Cu
Cu1+ Cu
Cu2+ Cu
Zn Zn
Zn2+ Zn
Ga Ga
Ga3+ Ga
Ge Ge
Ge4+ Ge
As As
Se Se
Br Br
Br1- Br
Kr Kr
Rb Rb
Rb1+ Rb
Sr Sr
Sr2+ Sr
Y Y
Y3+ Y
Zr Zr
Zr4+ Zr
Nb Nb
Nb3+ Nb
Nb5+ Nb
Mo Mo
Mo3+ Mo
Mo5+ Mo
Mo6+ Mo
Tc Tc
Ru Ru
Ru3+ Ru
Ru4+ Ru
Rh Rh
Rh3+ Rh
Rh4+ Rh
Pd Pd
Pd2+ Pd
Pd4+ Pd
Ag Ag
Ag1+ Ag
Ag2+ Ag
Cd Cd
Cd2+ Cd
In In
In3+ In
Sn Sn
Sn2+ Sn
Sn4+ Sn
Sb Sb
Sb3+ Sb
Sb5+ Sb
Te Te
I I
I1- I
Xe Xe
Cs Cs
Cs1+ Cs
Ba Ba
Ba2+ Ba
La La
La3+ La
Ce Ce
Ce3+ Ce
Ce4+ Ce
Pr Pr
Pr3+ Pr
Pr4+ Pr
Nd Nd
Nd3+ Nd
Pm Pm
Sm Sm
Sm3+ Sm
Eu Eu
Eu2+ Eu
Eu3+ Eu
Gd Gd
Gd3+ Gd
Tb Tb
Tb3+ Tb
Dy Dy
Dy3+ Dy
Ho Ho
Ho3+ Ho
Er Er
Er3+ Er
Tm Tm
Tm3+ Tm
Yb Yb
Yb2+ Yb
Yb3+ Yb
Lu Lu
Lu3+ Lu
Hf Hf
Hf4+ Hf
Ta Ta
Ta5+ Ta
W W
W6+ W
Re Re
Os Os
Os4+ Os
Ir Ir
Ir3+ Ir
Ir4+ Ir
Pt Pt
Pt2+ Pt
Pt4+ Pt
Au Au
Au1+ Au
Au3+ Au
Hg Hg
Hg1+ Hg
Hg2+ Hg
Tl Tl
TL1+ Tl
Tl3+ Tl
Pb Pb
Pb2+ Pb
Pb4+ Pb
Bi Bi
Bi3+ Bi
Bi5+ Bi
Po Po
At At
Rn Rn
Fr Fr
Ra Ra
Ra2+ Ra
Ac Ac
Ac3+ Ac
Th Th
Th4+ Th
Pa Pa
U U
U3+ U
U4+ U
U6+ U
Np Np
Np3+ Np
Np4+ Np
Np6+ Np
Pu Pu
Pu3+ Pu
Pu4+ Pu
Pu6+ Pu
Am Am
Cm Cm
Bk Bk
Cf Cf
save_
save__atom_type.key
_definition.id '_atom_type.key'
loop_
_alias.definition_id
'_atom_type.key'
_definition.update 2012-11-20
_description.text
;
Value is a unique key to a set of ATOM_TYPE items
in a looped list.
;
_name.category_id atom_type
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _atom_type.key = _atom_type.symbol'
save_
save__atom_type.number_in_cell
_definition.id '_atom_type.number_in_cell'
loop_
_alias.definition_id
'_atom_type.number_in_cell'
'_atom_type_number_in_cell'
_definition.update 2013-01-28
_description.text
;
Total number of atoms of this atom type in the unit cell.
;
_name.category_id atom_type
_name.object_id number_in_cell
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0:
_units.code none
loop_
_method.purpose
_method.expression
Evaluation
;
With t as atom_type
cnt = 0.
Loop a as atom_site {
if ( a.type_symbol == t.symbol ) {
cnt += a.occupancy * a.site_symmetry_multiplicity
} }
_atom_type.number_in_cell = cnt
;
save_
save__atom_type.oxidation_number
_definition.id '_atom_type.oxidation_number'
loop_
_alias.definition_id
'_atom_type.oxidation_number'
'_atom_type_oxidation_number'
_definition.update 2012-11-20
_description.text
;
Formal oxidation state of this atom type in the structure.
;
_name.category_id atom_type
_name.object_id oxidation_number
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Integer
_enumeration.range -8:8
_enumeration.default 0
save_
save__atom_type.radius_bond
_definition.id '_atom_type.radius_bond'
loop_
_alias.definition_id
'_atom_type.radius_bond'
'_atom_type_radius_bond'
_definition.update 2012-11-20
_description.text
;
The effective intra-molecular bonding radius of this atom type.
;
_name.category_id atom_type
_name.object_id radius_bond
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.def_index_id '_atom_type.symbol'
_enumeration.range 0.0:5.0
_units.code angstroms
loop_
_enumeration_default.index
_enumeration_default.value
H 0.37
D 0.37
H1- 0.37
He 0.40
Li 1.23
Li1+ 1.23
Be 0.89
Be2+ 0.89
B 0.80
C 0.77
N 0.74
O 0.74
O1- 0.74
F 0.72
F1- 0.72
Ne 0.72
Na 1.57
Na1+ 1.57
Mg 1.36
Mg2+ 1.36
Al 1.25
Al3+ 1.25
Si 1.17
Si4+ 1.17
P 1.10
S 1.04
Cl 0.99
Cl1- 0.99
Ar 1.00
K 2.03
K1+ 2.03
Ca 1.74
Ca2+ 1.74
Sc 1.44
Sc3+ 1.44
Ti 1.35
Ti2+ 1.35
Ti3+ 1.35
Ti4+ 1.35
V 1.22
V2+ 1.22
V3+ 1.22
V5+ 1.22
Cr 1.17
Cr2+ 1.17
Cr3+ 1.17
Mn 1.17
Mn2+ 1.17
Mn3+ 1.17
Mn4+ 1.17
Fe 1.17
Fe2+ 1.17
Fe3+ 1.17
Co 1.16
Co2+ 1.16
Co3+ 1.16
Ni 1.15
Ni2+ 1.15
Ni3+ 1.15
Cu 1.17
Cu1+ 1.17
Cu2+ 1.17
Zn 1.25
Zn2+ 1.25
Ga 1.25
Ga3+ 1.25
Ge 1.22
Ge4+ 1.22
As 1.21
Se 1.17
Br 1.14
Br1- 1.14
Kr 1.14
Rb 2.16
Rb1+ 2.16
Sr 1.91
Sr2+ 1.91
Y 1.62
Y3+ 1.62
Zr 1.45
Zr4+ 1.45
Nb 1.34
Nb3+ 1.34
Nb5+ 1.34
Mo 1.29
Mo3+ 1.29
Mo5+ 1.29
Mo6+ 1.29
Tc 1.27
Ru 1.24
Ru3+ 1.24
Ru4+ 1.24
Rh 1.25
Rh3+ 1.25
Rh4+ 1.25
Pd 1.28
Pd2+ 1.28
Pd4+ 1.28
Ag 1.34
Ag1+ 1.34
Ag2+ 1.34
Cd 1.41
Cd2+ 1.41
In 1.50
In3+ 1.50
Sn 1.41
Sn2+ 1.41
Sn4+ 1.41
Sb 1.41
Sb3+ 1.41
Sb5+ 1.41
Te 1.37
I 1.33
I1- 1.33
Xe 1.33
Cs 2.35
Cs1+ 2.35
Ba 1.98
Ba2+ 1.98
La 1.69
La3+ 1.69
Ce 1.65
Ce3+ 1.65
Ce4+ 1.65
Pr 1.65
Pr3+ 1.65
Pr4+ 1.65
Nd 1.64
Nd3+ 1.64
Pm 1.63
Sm 1.66
Sm3+ 1.66
Eu 1.85
Eu2+ 1.85
Eu3+ 1.85
Gd 1.61
Gd3+ 1.61
Tb 1.59
Tb3+ 1.59
Dy 1.59
Dy3+ 1.59
Ho 1.58
Ho3+ 1.58
Er 1.57
Er3+ 1.57
Tm 1.56
Tm3+ 1.56
Yb 1.70
Yb2+ 1.70
Yb3+ 1.70
Lu 1.56
Lu3+ 1.56
Hf 1.44
Hf4+ 1.44
Ta 1.34
Ta5+ 1.34
W 1.30
W6+ 1.30
Re 1.28
Os 1.26
Os4+ 1.26
Ir 1.26
Ir3+ 1.26
Ir4+ 1.26
Pt 1.29
Pt2+ 1.29
Pt4+ 1.29
Au 1.34
Au1+ 1.34
Au3+ 1.34
Hg 1.44
Hg1+ 1.44
Hg2+ 1.44
Tl 1.55
TL1+ 1.55
Tl3+ 1.55
Pb 1.54
Pb2+ 1.54
Pb4+ 1.54
Bi 1.52
Bi3+ 1.52
Bi5+ 1.52
Po 1.53
At 1.53
Rn 1.53
Fr 1.53
Ra 1.53
Ra2+ 1.53
Ac 1.53
Ac3+ 1.53
Th 1.65
Th4+ 1.65
Pa 1.53
U 1.42
U3+ 1.42
U4+ 1.42
U6+ 1.42
Np 1.42
Np3+ 1.42
Np4+ 1.42
Np6+ 1.42
Pu 1.42
Pu3+ 1.42
Pu4+ 1.42
Pu6+ 1.42
Am 1.42
Cm 1.42
Bk 1.42
Cf 1.42
save_
save__atom_type.radius_contact
_definition.id '_atom_type.radius_contact'
loop_
_alias.definition_id
'_atom_type.radius_contact'
'_atom_type_radius_contact'
_definition.update 2012-11-20
_description.text
;
The effective inter-molecular bonding radius of this atom type.
;
_name.category_id atom_type
_name.object_id radius_contact
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0.0:5.0
_units.code angstroms
loop_
_method.purpose
_method.expression
Evaluation
;
_atom_type.radius_contact = _atom_type.radius_bond + 1.25
;
save_
save__atom_type.symbol
_definition.id '_atom_type.symbol'
loop_
_alias.definition_id
'_atom_type.symbol'
'_atom_type_symbol'
_definition.update 2012-12-21
_description.text
;
The identity of the atom specie(s) representing this atom type.
Normally this code is the element symbol followed by the charge
if there is one. The symbol may be composed of any character except
an underline or a blank, with the proviso that digits designate an
oxidation state and must be followed by a + or - character.
;
_name.category_id atom_type
_name.object_id symbol
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_description_example.case
Mg
Cu2+
dummy
FeNi
save_
save_ATOM_TYPE_SCAT
_definition.id ATOM_TYPE_SCAT
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to describe atomic scattering
information used in crystallographic structure studies.
;
_name.category_id ATOM_TYPE
_name.object_id ATOM_TYPE_SCAT
_category.key_id '_atom_type_scat.key'
_category.key_list ['_atom_type_scat.symbol']
save_
save__atom_type_scat.Cromer_Mann_a1
_definition.id '_atom_type_scat.Cromer_Mann_a1'
loop_
_alias.definition_id
'_atom_type_scat.Cromer_Mann_a1'
'_atom_type_scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a1'
_name.category_id atom_type_scat
_name.object_id Cromer_Mann_a1
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items used to define Cromer-Mann coefficients
for generation of X-ray scattering factors.
Ref: International Tables for X-ray Crystallography, Vol. IV
(1974) Table 2.2B
or International Tables for Crystallography, Vol. C
(1991) Tables 6.1.1.4 and 6.1.1.5
;
_enumeration.def_index_id '_atom_type.symbol'
_type.source Assigned
_type.container Single
_definition.update 2012-11-29
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H .493002
D .493002
H1- .897661
He 0.8734
Li 1.1282
Li1+ .6968
Be 1.5919
Be2+ 6.2603
B 2.0545
C 2.31
N 12.2126
O 3.0485
O1- 4.1916
F 3.5392
F1- 3.6322
Ne 3.9553
Na 4.7626
Na1+ 3.2565
Mg 5.4204
Mg2+ 3.4988
Al 6.4202
Al3+ 4.17448
Si 6.2915
Si4+ 4.43918
P 6.4345
S 6.9053
Cl 11.4604
Cl1- 18.2915
Ar 7.4845
K 8.2186
K1+ 7.9578
Ca 8.6266
Ca2+ 15.6348
Sc 9.189
Sc3+ 13.4008
Ti 9.7595
Ti2+ 9.11423
Ti3+ 17.7344
Ti4+ 19.5114
V 10.2971
V2+ 10.106
V3+ 9.43141
V5+ 15.6887
Cr 10.6406
Cr2+ 9.54034
Cr3+ 9.6809
Mn 11.2819
Mn2+ 10.8061
Mn3+ 9.84521
Mn4+ 9.96253
Fe 11.7695
Fe2+ 11.0424
Fe3+ 11.1764
Co 12.2841
Co2+ 11.2296
Co3+ 10.338
Ni 12.8376
Ni2+ 11.4166
Ni3+ 10.7806
Cu 13.338
Cu1+ 11.9475
Cu2+ 11.8168
Zn 14.0743
Zn2+ 11.9719
Ga 15.2354
Ga3+ 12.692
Ge 16.0816
Ge4+ 12.9172
As 16.6723
Se 17.0006
Br 17.1789
Br1- 17.1718
Kr 17.3555
Rb 17.1784
Rb1+ 17.5816
Sr 17.5663
Sr2+ 18.0874
Y 17.776
Y3+ 17.9268
Zr 17.8765
Zr4+ 18.1668
Nb 17.6142
Nb3+ 19.8812
Nb5+ 17.9163
Mo 3.7025
Mo3+ 21.1664
Mo5+ 21.0149
Mo6+ 17.8871
Tc 19.1301
Ru 19.2674
Ru3+ 18.5638
Ru4+ 18.5003
Rh 19.2957
Rh3+ 18.8785
Rh4+ 18.8545
Pd 19.3319
Pd2+ 19.1701
Pd4+ 19.2493
Ag 19.2808
Ag1+ 19.1812
Ag2+ 19.1643
Cd 19.2214
Cd2+ 19.1514
In 19.1624
In3+ 19.1045
Sn 19.1889
Sn2+ 19.1094
Sn4+ 18.9333
Sb 19.6418
Sb3+ 18.9755
Sb5+ 19.8685
Te 19.9644
I 20.1472
I1- 20.2332
Xe 20.2933
Cs 20.3892
Cs1+ 20.3524
Ba 20.3361
Ba2+ 20.1807
La 20.578
La3+ 20.2489
Ce 21.1671
Ce3+ 20.8036
Ce4+ 20.3235
Pr 22.044
Pr3+ 21.3727
Pr4+ 20.9413
Nd 22.6845
Nd3+ 21.961
Pm 23.3405
Sm 24.0042
Sm3+ 23.1504
Eu 24.6274
Eu2+ 24.0063
Eu3+ 23.7497
Gd 25.0709
Gd3+ 24.3466
Tb 25.8976
Tb3+ 24.9559
Dy 26.507
Dy3+ 25.5395
Ho 26.9049
Ho3+ 26.1296
Er 27.6563
Er3+ 26.722
Tm 28.1819
Tm3+ 27.3083
Yb 28.6641
Yb2+ 28.1209
Yb3+ 27.8917
Lu 28.9476
Lu3+ 28.4628
Hf 29.144
Hf4+ 28.8131
Ta 29.2024
Ta5+ 29.1587
W 29.0818
W6+ 29.4936
Re 28.7621
Os 28.1894
Os4+ 30.419
Ir 27.3049
Ir3+ 30.4156
Ir4+ 30.7058
Pt 27.0059
Pt2+ 29.8429
Pt4+ 30.9612
Au 16.8819
Au1+ 28.0109
Au3+ 30.6886
Hg 20.6809
Hg1+ 25.0853
Hg2+ 29.5641
Tl 27.5446
TL1+ 21.3985
Tl3+ 30.8695
Pb 31.0617
Pb2+ 21.7886
Pb4+ 32.1244
Bi 33.3689
Bi3+ 21.8053
Bi5+ 33.5364
Po 34.6726
At 35.3163
Rn 35.5631
Fr 35.9299
Ra 35.7630
Ra2+ 35.2150
Ac 35.6597
Ac3+ 35.1736
Th 35.5645
Th4+ 35.1007
Pa 35.8847
U 36.0228
U3+ 35.5747
U4+ 35.3715
U6+ 34.8509
Np 36.1874
Np3+ 35.7074
Np4+ 35.5103
Np6+ 35.0136
Pu 36.5254
Pu3+ 35.8400
Pu4+ 35.6493
Pu6+ 35.1736
Am 36.6706
Cm 36.6488
Bk 36.7881
Cf 36.9185
save_
save__atom_type_scat.Cromer_Mann_a2
_definition.id '_atom_type_scat.Cromer_Mann_a2'
loop_
_alias.definition_id
'_atom_type_scat.Cromer_Mann_a2'
'_atom_type_scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a2'
_name.category_id atom_type_scat
_name.object_id Cromer_Mann_a2
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items used to define Cromer-Mann coefficients
for generation of X-ray scattering factors.
Ref: International Tables for X-ray Crystallography, Vol. IV
(1974) Table 2.2B
or International Tables for Crystallography, Vol. C
(1991) Tables 6.1.1.4 and 6.1.1.5
;
_enumeration.def_index_id '_atom_type.symbol'
_type.source Assigned
_type.container Single
_definition.update 2012-11-29
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H .322912
D .322912
H1- .565616
He 0.6309
Li .7508
Li1+ .7888
Be 1.1278
Be2+ .8849
B 1.3326
C 1.02
N 3.1322
O 2.2868
O1- 1.63969
F 2.6412
F1- 3.51057
Ne 3.1125
Na 3.1736
Na1+ 3.9362
Mg 2.1735
Mg2+ 3.8378
Al 1.9002
Al3+ 3.3876
Si 3.0353
Si4+ 3.20345
P 4.1791
S 5.2034
Cl 7.1964
Cl1- 7.2084
Ar 6.6623
K 7.4398
K1+ 7.4917
Ca 7.3873
Ca2+ 7.9518
Sc 7.3679
Sc3+ 8.0273
Ti 7.3558
Ti2+ 7.62174
Ti3+ 8.73816
Ti4+ 8.23473
V 7.3511
V2+ 7.3541
V3+ 7.7419
V5+ 8.14208
Cr 7.3537
Cr2+ 7.7509
Cr3+ 7.81136
Mn 7.3573
Mn2+ 7.362
Mn3+ 7.87194
Mn4+ 7.97057
Fe 7.3573
Fe2+ 7.374
Fe3+ 7.3863
Co 7.3409
Co2+ 7.3883
Co3+ 7.88173
Ni 7.292
Ni2+ 7.4005
Ni3+ 7.75868
Cu 7.1676
Cu1+ 7.3573
Cu2+ 7.11181
Zn 7.0318
Zn2+ 7.3862
Ga 6.7006
Ga3+ 6.69883
Ge 6.3747
Ge4+ 6.70003
As 6.0701
Se 5.8196
Br 5.2358
Br1- 6.3338
Kr 6.7286
Rb 9.6435
Rb1+ 7.6598
Sr 9.8184
Sr2+ 8.1373
Y 10.2946
Y3+ 9.1531
Zr 10.948
Zr4+ 10.0562
Nb 12.0144
Nb3+ 18.0653
Nb5+ 13.3417
Mo 17.2356
Mo3+ 18.2017
Mo5+ 18.0992
Mo6+ 11.175
Tc 11.0948
Ru 12.9182
Ru3+ 13.2885
Ru4+ 13.1787
Rh 14.3501
Rh3+ 14.1259
Rh4+ 13.9806
Pd 15.5017
Pd2+ 15.2096
Pd4+ 14.79
Ag 16.6885
Ag1+ 15.9719
Ag2+ 16.2456
Cd 17.6444
Cd2+ 17.2535
In 18.5596
In3+ 18.1108
Sn 19.1005
Sn2+ 19.0548
Sn4+ 19.7131
Sb 19.0455
Sb3+ 18.933
Sb5+ 19.0302
Te 19.0138
I 18.9949
I1- 18.997
Xe 19.0298
Cs 19.1062
Cs1+ 19.1278
Ba 19.297
Ba2+ 19.1136
La 19.599
La3+ 19.3763
Ce 19.7695
Ce3+ 19.559
Ce4+ 19.8186
Pr 19.6697
Pr3+ 19.7491
Pr4+ 20.0539
Nd 19.6847
Nd3+ 19.9339
Pm 19.6095
Sm 19.4258
Sm3+ 20.2599
Eu 19.0886
Eu2+ 19.9504
Eu3+ 20.3745
Gd 19.0798
Gd3+ 20.4208
Tb 18.2185
Tb3+ 20.3271
Dy 17.6383
Dy3+ 20.2861
Ho 17.294
Ho3+ 20.0994
Er 16.4285
Er3+ 19.7748
Tm 15.8851
Tm3+ 19.332
Yb 15.4345
Yb2+ 17.6817
Yb3+ 18.7614
Lu 15.2208
Lu3+ 18.121
Hf 15.1726
Hf4+ 18.4601
Ta 15.2293
Ta5+ 18.8407
W 15.43
W6+ 19.3763
Re 15.7189
Os 16.155
Os4+ 15.2637
Ir 16.7296
Ir3+ 15.862
Ir4+ 15.5512
Pt 17.7639
Pt2+ 16.7224
Pt4+ 15.9829
Au 18.5913
Au1+ 17.8204
Au3+ 16.9029
Hg 19.0417
Hg1+ 18.4973
Hg2+ 18.06
Tl 19.1584
TL1+ 20.4723
Tl3+ 18.3841
Pb 13.0637
Pb2+ 19.5682
Pb4+ 18.8003
Bi 12.951
Bi3+ 19.5026
Bi5+ 25.0946
Po 15.4733
At 19.0211
Rn 21.2816
Fr 23.0547
Ra 22.9064
Ra2+ 21.6700
Ac 23.1032
Ac3+ 22.1112
Th 23.4219
Th4+ 22.4418
Pa 23.2948
U 23.4128
U3+ 22.5259
U4+ 22.5326
U6+ 22.7584
Np 23.5964
Np3+ 22.6130
Np4+ 22.5787
Np6+ 22.7286
Pu 23.8083
Pu3+ 22.7169
Pu4+ 22.6460
Pu6+ 22.7181
Am 24.0992
Cm 24.4096
Bk 24.7736
Cf 25.1995
save_
save__atom_type_scat.Cromer_Mann_a3
_definition.id '_atom_type_scat.Cromer_Mann_a3'
loop_
_alias.definition_id
'_atom_type_scat.Cromer_Mann_a3'
'_atom_type_scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_a3'
_name.category_id atom_type_scat
_name.object_id Cromer_Mann_a3
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items used to define Cromer-Mann coefficients
for generation of X-ray scattering factors.
Ref: International Tables for X-ray Crystallography, Vol. IV
(1974) Table 2.2B
or International Tables for Crystallography, Vol. C
(1991) Tables 6.1.1.4 and 6.1.1.5
;
_enumeration.def_index_id '_atom_type.symbol'
_type.source Assigned
_type.container Single
_definition.update 2012-11-29
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H .140191
D .140191
H1- .415815
He 0.3112
Li .6175
Li1+ .3414
Be .5391
Be2+ .7993
B 1.0979
C 1.5886
N 2.0125
O 1.5463
O1- 1.52673
F 1.517
F1- 1.26064
Ne 1.4546
Na 1.2674
Na1+ 1.3998
Mg 1.2269
Mg2+ 1.3284
Al 1.5936
Al3+ 1.20296
Si 1.9891
Si4+ 1.19453
P 1.78
S 1.4379
Cl 6.2556
Cl1- 6.5337
Ar 0.6539
K 1.0519
K1+ 6.359
Ca 1.5899
Ca2+ 8.4372
Sc 1.6409
Sc3+ 1.65943
Ti 1.6991
Ti2+ 2.2793
Ti3+ 5.25691
Ti4+ 2.01341
V 2.0703
V2+ 2.2884
V3+ 2.15343
V5+ 2.03081
Cr 3.324
Cr2+ 3.58274
Cr3+ 2.87603
Mn 3.0193
Mn2+ 3.5268
Mn3+ 3.56531
Mn4+ 2.76067
Fe 3.5222
Fe2+ 4.1346
Fe3+ 3.3948
Co 4.0034
Co2+ 4.7393
Co3+ 4.76795
Ni 4.4438
Ni2+ 5.3442
Ni3+ 5.22746
Cu 5.6158
Cu1+ 6.2455
Cu2+ 5.78135
Zn 5.1652
Zn2+ 6.4668
Ga 4.3591
Ga3+ 6.06692
Ge 3.7068
Ge4+ 6.06791
As 3.4313
Se 3.9731
Br 5.6377
Br1- 5.5754
Kr 5.5493
Rb 5.1399
Rb1+ 5.8981
Sr 5.422
Sr2+ 2.5654
Y 5.72629
Y3+ 1.76795
Zr 5.41732
Zr4+ 1.01118
Nb 4.04183
Nb3+ 11.0177
Nb5+ 10.799
Mo 12.8876
Mo3+ 11.7423
Mo5+ 11.4632
Mo6+ 6.57891
Tc 4.64901
Ru 4.86337
Ru3+ 9.32602
Ru4+ 4.71304
Rh 4.73425
Rh3+ 3.32515
Rh4+ 2.53464
Pd 5.29537
Pd2+ 4.32234
Pd4+ 2.89289
Ag 4.8045
Ag1+ 5.27475
Ag2+ 4.3709
Cd 4.461
Cd2+ 4.47128
In 4.2948
In3+ 3.78897
Sn 4.4585
Sn2+ 4.5648
Sn4+ 3.4182
Sb 5.0371
Sb3+ 5.10789
Sb5+ 2.41253
Te 6.14487
I 7.5138
I1- 7.8069
Xe 8.9767
Cs 10.662
Cs1+ 10.2821
Ba 10.888
Ba2+ 10.9054
La 11.3727
La3+ 11.6323
Ce 11.8513
Ce3+ 11.9369
Ce4+ 12.1233
Pr 12.3856
Pr3+ 12.1329
Pr4+ 12.4668
Nd 12.774
Nd3+ 12.12
Pm 13.1235
Sm 13.4396
Sm3+ 11.9202
Eu 13.7603
Eu2+ 11.8034
Eu3+ 11.8509
Gd 13.8518
Gd3+ 11.8708
Tb 14.3167
Tb3+ 12.2471
Dy 14.5596
Dy3+ 11.9812
Ho 14.5583
Ho3+ 11.9788
Er 14.9779
Er3+ 12.1506
Tm 15.1542
Tm3+ 12.3339
Yb 15.3087
Yb2+ 13.3335
Yb3+ 12.6072
Lu 15.1
Lu3+ 12.8429
Hf 14.7586
Hf4+ 12.7285
Ta 14.5135
Ta5+ 12.8268
W 14.4327
W6+ 13.0544
Re 14.5564
Os 14.9305
Os4+ 14.7458
Ir 15.6115
Ir3+ 13.6145
Ir4+ 14.2326
Pt 15.7131
Pt2+ 13.2153
Pt4+ 13.7348
Au 25.5582
Au1+ 14.3359
Au3+ 12.7801
Hg 21.6575
Hg1+ 16.8883
Hg2+ 12.8374
Tl 15.538
TL1+ 18.7478
Tl3+ 11.9328
Pb 18.442
Pb2+ 19.1406
Pb4+ 12.0175
Bi 16.5877
Bi3+ 19.1053
Bi5+ 19.2497
Po 13.1138
At 9.49887
Rn 8.0037
Fr 12.1439
Ra 12.4739
Ra2+ 7.91342
Ac 12.5977
Ac3+ 8.19216
Th 12.7473
Th4+ 9.78554
Pa 14.1891
U 14.9491
U3+ 12.2165
U4+ 12.0291
U6+ 14.0099
Np 15.6402
Np3+ 12.9898
Np4+ 12.7766
Np6+ 14.3884
Pu 16.7707
Pu3+ 13.5807
Pu4+ 13.3595
Pu6+ 14.7635
Am 17.3415
Cm 17.3990
Bk 17.8919
Cf 18.3317
save_
save__atom_type_scat.Cromer_Mann_a4
_definition.id '_atom_type_scat.Cromer_Mann_a4'
loop_
_alias.definition_id
'_atom_type_scat.Cromer_Mann_a4'
'_atom_type_scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_a4'
_name.category_id atom_type_scat
_name.object_id Cromer_Mann_a4
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items used to define Cromer-Mann coefficients
for generation of X-ray scattering factors.
Ref: International Tables for X-ray Crystallography, Vol. IV
(1974) Table 2.2B
or International Tables for Crystallography, Vol. C
(1991) Tables 6.1.1.4 and 6.1.1.5
;
_enumeration.def_index_id '_atom_type.symbol'
_type.source Assigned
_type.container Single
_definition.update 2012-11-29
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H .04081
D .04081
H1- .116973
He 0.178
Li .4653
Li1+ .1563
Be .7029
Be2+ .1647
B .7068
C .865
N 1.1663
O .867
O1- -20.307
F 1.0243
F1- .940706
Ne 1.1251
Na 1.1128
Na1+ 1.0032
Mg 2.3073
Mg2+ .8497
Al 1.9646
Al3+ .528137
Si 1.541
Si4+ .41653
P 1.4908
S 1.5863
Cl 1.6455
Cl1- 2.3386
Ar 1.6442
K .8659
K1+ 1.1915
Ca 1.0211
Ca2+ .8537
Sc 1.468
Sc3+ 1.57936
Ti 1.9021
Ti2+ .087899
Ti3+ 1.92134
Ti4+ 1.5208
V 2.0571
V2+ .0223
V3+ .016865
V5+ -9.576
Cr 1.4922
Cr2+ .509107
Cr3+ .113575
Mn 2.2441
Mn2+ .2184
Mn3+ .323613
Mn4+ .054447
Fe 2.3045
Fe2+ .4399
Fe3+ .0724
Co 2.3488
Co2+ .7108
Co3+ .725591
Ni 2.38
Ni2+ .9773
Ni3+ .847114
Cu 1.6735
Cu1+ 1.5578
Cu+ 1.14523
Zn 2.41
Zn2+ 1.394
Ga 2.9623
Ga3+ 1.0066
Ge 3.683
Ge4+ .859041
As 4.2779
Se 4.3543
Br 3.9851
Br1- 3.7272
Kr 3.5375
Rb 1.5292
Rb1+ 2.7817
Sr 2.6694
Sr2+ -34.193
Y 3.26588
Y3+ -33.108
Zr 3.65721
Zr4+ -2.6479
Nb 3.53346
Nb3+ 1.94715
Nb5+ .337905
Mo 3.7429
Mo3+ 2.30951
Mo5+ .740625
Mo6+ 0.
Tc 2.71263
Ru 1.56756
Ru3+ 3.00964
Ru4+ 2.18535
Rh 1.28918
Rh3+ -6.1989
Rh4+ -5.6526
Pd .605844
Pd2+ 0.
Pd4+ -7.9492
Ag 1.0463
Ag1+ .357534
Ag2+ 0.
Cd 1.6029
Cd2+ 0.
In 2.0396
In3+ 0.
Sn 2.4663
Sn2+ .487
Sn4+ .0193
Sb 2.6827
Sb3+ .288753
Sb5+ 0.
Te 2.5239
I 2.2735
I1- 2.8868
Xe 1.99
Cs 1.4953
Cs1+ .9615
Ba 2.6959
Ba2+ .773634
La 3.28719
La3+ .336048
Ce 3.33049
Ce3+ .612376
Ce4+ .144583
Pr 2.82428
Pr3+ .97518
Pr4+ .296689
Nd 2.85137
Nd3+ 1.51031
Pm 2.87516
Sm 2.89604
Sm3+ 2.71488
Eu 2.9227
Eu2+ 3.87243
Eu3+ 3.26503
Gd 3.54545
Gd3+ 3.7149
Tb 2.95354
Tb3+ 3.773
Dy 2.96577
Dy3+ 4.50073
Ho 3.63837
Ho3+ 4.93676
Er 2.98233
Er3+ 5.17379
Tm 2.98706
Tm3+ 5.38348
Yb 2.98963
Yb2+ 5.14657
Yb3+ 5.47647
Lu 3.71601
Lu3+ 5.59415
Hf 4.30013
Hf4+ 5.59927
Ta 4.76492
Ta5+ 5.38695
W 5.11982
W6+ 5.06412
Re 5.44174
Os 5.67589
Os4+ 5.06795
Ir 5.83377
Ir3+ 5.82008
Ir4+ 5.53672
Pt 5.7837
Pt2+ 6.35234
Pt4+ 5.92034
Au 5.86
Au1+ 6.58077
Au3+ 6.52354
Hg 5.9676
Hg1+ 6.48216
Hg2+ 6.89912
Tl 5.52593
TL1+ 6.82847
Tl3+ 7.00574
Pb 5.9696
Pb2+ 7.01107
Pb4+ 6.96886
Bi 6.4692
Bi3+ 7.10295
Bi5+ 6.91555
Po 7.02588
At 7.42518
Rn 7.4433
Fr 2.11253
Ra 3.21097
Ra2+ 7.65078
Ac 4.08655
Ac3+ 7.05545
Th 4.80703
Th4+ 5.29444
Pa 4.17287
U 4.1880
U3+ 5.37073
U4+ 4.79840
U6+ 1.21457
Np 4.18550
Np3+ 5.43227
Np4+ 4.92159
Np6+ 1.75669
Pu 3.47947
Pu3+ 5.66016
Pu4+ 5.18831
Pu6+ 2.28678
Am 3.49331
Cm 4.21665
Bk 4.23284
Cf 4.24391
save_
save__atom_type_scat.Cromer_Mann_b1
_definition.id '_atom_type_scat.Cromer_Mann_b1'
loop_
_alias.definition_id
'_atom_type_scat.Cromer_Mann_b1'
'_atom_type_scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b1'
_name.category_id atom_type_scat
_name.object_id Cromer_Mann_b1
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items used to define Cromer-Mann coefficients
for generation of X-ray scattering factors.
Ref: International Tables for X-ray Crystallography, Vol. IV
(1974) Table 2.2B
or International Tables for Crystallography, Vol. C
(1991) Tables 6.1.1.4 and 6.1.1.5
;
_enumeration.def_index_id '_atom_type.symbol'
_type.source Assigned
_type.container Single
_definition.update 2012-11-29
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H 10.5109
D 10.5109
H1- 53.1368
He 9.1037
Li 3.9546
Li1+ 4.6237
Be 43.6427
Be2+ .0027
B 23.2185
C 20.8439
N .0057
O 13.2771
O1- 12.8573
F 10.2825
F1- 5.27756
Ne 8.4042
Na 3.285
Na1+ 2.6671
Mg 2.8275
Mg2+ 2.1676
Al 3.0387
Al3+ 1.93816
Si 2.4386
Si4+ 1.64167
P 1.9067
S 1.4679
Cl .0104
Cl1- .0066
Ar 0.9072
K 12.7949
K1+ 12.6331
Ca 10.4421
Ca2+ -.0074
Sc 9.0213
Sc3+ .29854
Ti 7.8508
Ti2+ 7.5243
Ti3+ .22061
Ti4+ .178847
V 6.8657
V2+ 6.8818
V3+ 6.39535
V5+ .679003
Cr 6.1038
Cr2+ 5.66078
Cr3+ 5.59463
Mn 5.3409
Mn2+ 5.2796
Mn3+ 4.91797
Mn4+ 4.8485
Fe 4.7611
Fe2+ 4.6538
Fe3+ 4.6147
Co 4.2791
Co2+ 4.1231
Co3+ 3.90969
Ni 3.8785
Ni2+ 3.6766
Ni3+ 3.5477
Cu 3.5828
Cu1+ 3.3669
Cu2+ 3.37484
Zn 3.2655
Zn2+ 2.9946
Ga 3.0669
Ga3+ 2.81262
Ge 2.8509
Ge4+ 2.53718
As 2.6345
Se 2.4098
Br 2.1723
Br1- 2.2059
Kr 1.9384
Rb 1.7888
Rb1+ 1.7139
Sr 1.5564
Sr2+ 1.4907
Y 1.4029
Y3+ 1.35417
Zr 1.27618
Zr4+ 1.2148
Nb 1.18865
Nb3+ .019175
Nb5+ 1.12446
Mo .2772
Mo3+ .014734
Mo5+ .014345
Mo6+ 1.03649
Tc .864132
Ru .80852
Ru3+ .847329
Ru4+ .844582
Rh .751536
Rh3+ .764252
Rh4+ .760825
Pd .698655
Pd2+ .696219
Pd4+ .683839
Ag .6446
Ag1+ .646179
Ag2+ .645643
Cd .5946
Cd2+ .597922
In .5476
In3+ .551522
Sn 5.8303
Sn2+ .5036
Sn4+ 5.764
Sb 5.3034
Sb3+ .467196
Sb5+ 5.44853
Te 4.81742
I 4.347
I1- 4.3579
Xe 3.9282
Cs 3.569
Cs1+ 3.552
Ba 3.216
Ba2+ 3.21367
La 2.94817
La3+ 2.9207
Ce 2.81219
Ce3+ 2.77691
Ce4+ 2.65941
Pr 2.77393
Pr3+ 2.6452
Pr4+ 2.54467
Nd 2.66248
Nd3+ 2.52722
Pm 2.5627
Sm 2.47274
Sm3+ 2.31641
Eu 2.3879
Eu2+ 2.27783
Eu3+ 2.22258
Gd 2.25341
Gd3+ 2.13553
Tb 2.24256
Tb3+ 2.05601
Dy 2.1802
Dy3+ 1.9804
Ho 2.07051
Ho3+ 1.91072
Er 2.07356
Er3+ 1.84659
Tm 2.02859
Tm3+ 1.78711
Yb 1.9889
Yb2+ 1.78503
Yb3+ 1.73272
Lu 1.90182
Lu3+ 1.68216
Hf 1.83262
Hf4+ 1.59136
Ta 1.77333
Ta5+ 1.50711
W 1.72029
W6+ 1.42755
Re 1.67191
Os 1.62903
Os4+ 1.37113
Ir 1.59279
Ir3+ 1.34323
Ir4+ 1.30923
Pt 1.51293
Pt2+ 1.32927
Pt4+ 1.24813
Au .4611
Au1+ 1.35321
Au3+ 1.2199
Hg .545
Hg1+ 1.39507
Hg2+ 1.21152
Tl .65515
TL1+ 1.4711
Tl3+ 1.1008
Pb .6902
Pb2+ 1.3366
Pb4+ 1.00566
Bi .704
Bi3+ 1.2356
Bi5+ .91654
Po .700999
At .685870
Rn .6631
Fr .646453
Ra .616341
Ra2+ .604909
Ac .589092
Ac3+ .579689
Th .563359
Th4+ .555054
Pa .547751
U .5293
U3+ .520480
U4+ .516598
U6+ .507079
Np .511929
Np3+ .502322
Np4+ .498626
Np6+ .489810
Pu .499384
Pu3+ .484938
Pu4+ .481422
Pu6+ .473204
Am .483629
Cm .465154
Bk .451018
Cf .437533
save_
save__atom_type_scat.Cromer_Mann_b2
_definition.id '_atom_type_scat.Cromer_Mann_b2'
loop_
_alias.definition_id
'_atom_type_scat.Cromer_Mann_b2'
'_atom_type_scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b2'
_name.category_id atom_type_scat
_name.object_id Cromer_Mann_b2
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items used to define Cromer-Mann coefficients
for generation of X-ray scattering factors.
Ref: International Tables for X-ray Crystallography, Vol. IV
(1974) Table 2.2B
or International Tables for Crystallography, Vol. C
(1991) Tables 6.1.1.4 and 6.1.1.5
;
_enumeration.def_index_id '_atom_type.symbol'
_type.source Assigned
_type.container Single
_definition.update 2012-11-29
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H 26.1257
D 26.1257
H1- 15.187
He 3.3568
Li 1.0524
Li1+ 1.9557
Be 1.8623
Be2+ .8313
B 1.021
C 10.2075
N 9.8933
O 5.7011
O1- 4.17236
F 4.2944
F1- 14.7353
Ne 3.4262
Na 8.8422
Na1+ 6.1153
Mg 79.2611
Mg2+ 4.7542
Al .7426
Al3+ 4.14553
Si 32.3337
Si4+ 3.43757
P 27.157
S 22.2151
Cl 1.1662
Cl1- 1.1717
Ar 14.8407
K .7748
K1+ .7674
Ca .6599
Ca2+ .6089
Sc .5729
Sc3+ 7.9629
Ti .5
Ti2+ .457585
Ti3+ 7.04716
Ti4+ 6.67018
V .4385
V2+ .4409
V3+ .383349
V5+ 5.40135
Cr .392
Cr2+ .344261
Cr3+ .334393
Mn .3432
Mn2+ .3435
Mn3+ .294393
Mn4+ .283303
Fe .3072
Fe2+ .3053
Fe3+ .3005
Co .2784
Co2+ .2726
Co3+ .238668
Ni .2565
Ni2+ .2449
Ni3+ .22314
Cu .247
Cu1+ .2274
Cu2+ .244078
Zn .2333
Zn2+ .2031
Ga .2412
Ga3+ .22789
Ge .2516
Ge4+ .205855
As .2647
Se .2726
Br 16.5796
Br1- 19.3345
Kr 16.5623
Rb 17.3151
Rb1+ 14.7957
Sr 14.0988
Sr2+ 12.6963
Y 12.8006
Y3+ 11.2145
Zr 11.916
Zr4+ 10.1483
Nb 11.766
Nb3+ 1.13305
Nb5+ .028781
Mo 1.0958
Mo3+ 1.03031
Mo5+ 1.02238
Mo6+ 8.48061
Tc 8.14487
Ru 8.43467
Ru3+ 8.37164
Ru4+ 8.12534
Rh 8.21758
Rh3+ 7.84438
Rh4+ 7.62436
Pd 7.98929
Pd2+ 7.55573
Pd4+ 7.14833
Ag 7.4726
Ag1+ 7.19123
Ag2+ 7.18544
Cd 6.9089
Cd2+ 6.80639
In 6.3776
In3+ 6.3247
Sn .5031
Sn2+ 5.8378
Sn4+ .4655
Sb .4607
Sb3+ 5.22126
Sb5+ .467973
Te .420885
I .3814
I1- .3815
Xe 0.344
Cs .3107
Cs1+ .3086
Ba .2756
Ba2+ .28331
La .244475
La3+ .250698
Ce .226836
Ce3+ .23154
Ce4+ .21885
Pr .222087
Pr3+ .214299
Pr4+ .202481
Nd .210628
Nd3+ .199237
Pm 0.202088
Sm .196451
Sm3+ .174081
Eu .1942
Eu2+ .17353
Eu3+ .16394
Gd .181951
Gd3+ .155525
Tb .196143
Tb3+ .149525
Dy .202172
Dy3+ .143384
Ho .19794
Ho3+ .139358
Er .223545
Er3+ .13729
Tm .238849
Tm3+ .136974
Yb .25711
Yb2+ .15997
Yb3+ .13879
Lu 9.98519
Lu3+ .142292
Hf 9.5999
Hf4+ .128903
Ta 9.37046
Ta5+ .116741
W 9.2259
W6+ .104621
Re 9.09227
Os 8.97948
Os4+ 6.84706
Ir 8.86553
Ir3+ 7.10909
Ir4+ 6.71983
Pt 8.81174
Pt2+ 7.38979
Pt4+ 6.60834
Au 8.6216
Au1+ 7.7395
Au3+ 6.82872
Hg 8.4484
Hg1+ 7.65105
Hg2+ 7.05639
Tl 8.70751
TL1+ .517394
Tl3+ 6.53852
Pb 2.3576
Pb2+ .488383
Pb4+ 6.10926
Bi 2.9238
Bi3+ 6.24149
Bi5+ .039042
Po 3.55078
At 3.97458
Rn 4.0691
Fr 4.17619
Ra 3.87135
Ra2+ 3.57670
Ac 3.65155
Ac3+ 3.41437
Th 3.46204
Th4+ 3.24498
Pa 3.41519
U 3.3253
U3+ 3.12293
U4+ 3.05053
U6+ 2.89030
Np 3.25396
Np3+ 3.03807
Np4+ 2.96627
Np6+ 2.81099
Pu 3.26371
Pu3+ 2.96118
Pu4+ 2.89020
Pu6+ 2.73848
Am 3.20647
Cm 3.08997
Bk 3.04619
Cf 3.00775
save_
save__atom_type_scat.Cromer_Mann_b3
_definition.id '_atom_type_scat.Cromer_Mann_b3'
loop_
_alias.definition_id
'_atom_type_scat.Cromer_Mann_b3'
'_atom_type_scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_b3'
_name.category_id atom_type_scat
_name.object_id Cromer_Mann_b3
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items used to define Cromer-Mann coefficients
for generation of X-ray scattering factors.
Ref: International Tables for X-ray Crystallography, Vol. IV
(1974) Table 2.2B
or International Tables for Crystallography, Vol. C
(1991) Tables 6.1.1.4 and 6.1.1.5
;
_enumeration.def_index_id '_atom_type.symbol'
_type.source Assigned
_type.container Single
_definition.update 2012-11-29
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H 3.14236
D 3.14236
H1- 186.576
He 22.9276
Li 85.3905
Li1+ .6316
Be 103.483
Be2+ 2.2758
B 60.3498
C .5687
N 28.9975
O .3239
O1- 47.0179
F .2615
F1- .442258
Ne 0.2306
Na .3136
Na1+ .2001
Mg .3808
Mg2+ .185
Al 31.5472
Al3+ .228753
Si .6785
Si4+ .2149
P .526
S .2536
Cl 18.5194
Cl1- 19.5424
Ar 43.8983
K 213.187
K1+ -.002
Ca 85.7484
Ca2+ 10.3116
Sc 136.108
Sc3+ -.28604
Ti 35.6338
Ti2+ 19.5361
Ti3+ -.15762
Ti4+ -.29263
V 26.8938
V2+ 20.3004
V3+ 15.1908
V5+ 9.97278
Cr 20.2626
Cr2+ 13.3075
Cr3+ 12.8288
Mn 17.8674
Mn2+ 14.343
Mn3+ 10.8171
Mn4+ 10.4852
Fe 15.3535
Fe2+ 12.0546
Fe3+ 11.6729
Co 13.5359
Co2+ 10.2443
Co3+ 8.35583
Ni 12.1763
Ni2+ 8.873
Ni3+ 7.64468
Cu 11.3966
Cu1+ 8.6625
Cu2+ 7.9876
Zn 10.3163
Zn2+ 7.0826
Ga 10.7805
Ga3+ 6.36441
Ge 11.4468
Ge4+ 5.47913
As 12.9479
Se 15.2372
Br .2609
Br1- .2871
Kr 0.2261
Rb .2748
Rb1+ .1603
Sr .1664
Sr2+ 24.5651
Y .125599
Y3+ 22.6599
Zr .117622
Zr4+ 21.6054
Nb .204785
Nb3+ 10.1621
Nb5+ 9.28206
Mo 11.004
Mo3+ 9.53659
Mo5+ 8.78809
Mo6+ .058881
Tc 21.5707
Ru 24.7997
Ru3+ .017662
Ru4+ .036495
Rh 25.8749
Rh3+ 21.2487
Rh4+ 19.3317
Pd 25.2052
Pd2+ 22.5057
Pd4+ 17.9144
Ag 24.6605
Ag1+ 21.7326
Ag2+ 21.4072
Cd 24.7008
Cd2+ 20.2521
In 25.8499
In3+ 17.3595
Sn 26.8909
Sn2+ 23.3752
Sn4+ 14.0049
Sb 27.9074
Sb3+ 19.5902
Sb5+ 14.1259
Te 28.5284
I 27.766
I1- 29.5259
Xe 26.4659
Cs 24.3879
Cs1+ 23.7128
Ba 20.2073
Ba2+ 20.0558
La 18.7726
La3+ 17.8211
Ce 17.6083
Ce3+ 16.5408
Ce4+ 15.7992
Pr 16.7669
Pr3+ 15.323
Pr4+ 14.8137
Nd 15.885
Nd3+ 14.1783
Pm 15.1009
Sm 14.3996
Sm3+ 12.1571
Eu 13.7546
Eu2+ 11.6096
Eu3+ 11.311
Gd 12.9331
Gd3+ 10.5782
Tb 12.6648
Tb3+ 10.0499
Dy 12.1899
Dy3+ 9.34972
Ho 11.4407
Ho3+ 8.80018
Er 11.3604
Er3+ 8.36225
Tm 10.9975
Tm3+ 7.96778
Yb 10.6647
Yb2+ 8.18304
Yb3+ 7.64412
Lu .261033
Lu3+ 7.33727
Hf .275116
Hf4+ 6.76232
Ta .295977
Ta5+ 6.31524
W .321703
W6+ 5.93667
Re .3505
Os .382661
Os4+ .165191
Ir .417916
Ir3+ .204633
Ir4+ .167252
Pt .424593
Pt2+ .263297
Pt4+ .16864
Au 1.4826
Au1+ .356752
Au3+ .212867
Hg 1.5729
Hg1+ .443378
Hg2+ .284738
Tl 1.96347
TL1+ 7.43463
Tl3+ .219074
Pb 8.618
Pb2+ 6.7727
Pb4+ .147041
Bi 8.7937
Bi3+ .469999
Bi5+ 5.71414
Po 9.55642
At 11.3824
Rn 14.0422
Fr 23.1052
Ra 19.9887
Ra2+ 12.6010
Ac 18.5990
Ac3+ 12.9187
Th 17.8309
Th4+ 13.4661
Pa 16.9235
U 16.0927
U3+ 12.7148
U4+ 12.5723
U6+ 13.1767
Np 15.3622
Np3+ 12.1449
Np4+ 11.9484
Np6+ 12.3300
Pu 14.9455
Pu3+ 11.5331
Pu4+ 11.3160
Pu6+ 11.5530
Am 14.3136
Cm 13.4346
Bk 12.8946
Cf 12.4044
save_
save__atom_type_scat.Cromer_Mann_b4
_definition.id '_atom_type_scat.Cromer_Mann_b4'
loop_
_alias.definition_id
'_atom_type_scat.Cromer_Mann_b4'
'_atom_type_scat_Cromer_Mann_b4'
'_atom_type.scat_Cromer_Mann_b4'
_name.category_id atom_type_scat
_name.object_id Cromer_Mann_b4
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items used to define Cromer-Mann coefficients
for generation of X-ray scattering factors.
Ref: International Tables for X-ray Crystallography, Vol. IV
(1974) Table 2.2B
or International Tables for Crystallography, Vol. C
(1991) Tables 6.1.1.4 and 6.1.1.5
;
_enumeration.def_index_id '_atom_type.symbol'
_type.source Assigned
_type.container Single
_definition.update 2012-11-29
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H 57.7997
D 57.7997
H1- 3.56709
He 0.9821
Li 168.261
Li1+ 10.0953
Be .542
Be2+ 5.1146
B .1403
C 51.6512
N .5826
O 32.9089
O1- -.01404
F 26.1476
F1- 47.3437
Ne 21.7814
Na 129.424
Na1+ 14.039
Mg 7.1937
Mg2+ 10.1411
Al 85.0886
Al3+ 8.28524
Si 81.6937
Si4+ 6.65365
P 68.1645
S 56.172
Cl 47.7784
Cl1- 60.4486
Ar 33.3929
K 41.6841
K1+ 31.9128
Ca 178.437
Ca2+ 25.9905
Sc 51.3531
Sc3+ 16.0662
Ti 116.105
Ti2+ 61.6558
Ti3+ 15.9768
Ti4+ 12.9464
V 102.478
V2+ 115.122
V3+ 63.969
V5+ .940464
Cr 98.7399
Cr2+ 32.4224
Cr3+ 32.8761
Mn 83.7543
Mn2+ 41.3235
Mn3+ 24.1281
Mn4+ 27.573
Fe 76.8805
Fe2+ 31.2809
Fe3+ 38.5566
Co 71.1692
Co2+ 25.6466
Co3+ 18.3491
Ni 66.3421
Ni2+ 22.1626
Ni3+ 16.9673
Cu 64.8126
Cu1+ 25.8487
Cu2+ 19.897
Zn 58.7097
Zn2+ 18.0995
Ga 61.4135
Ga3+ 14.4122
Ge 54.7625
Ge4+ 11.603
As 47.7972
Se 43.8163
Br 41.4328
Br1- 58.1535
Kr 39.3972
Rb 164.934
Rb1+ 31.2087
Sr 132.376
Sr2+ -.0138
Y 104.354
Y3+ -.01319
Zr 87.6627
Zr4+ -.10276
Nb 69.7957
Nb3+ 28.3389
Nb5+ 25.7228
Mo 61.6584
Mo3+ 26.6307
Mo5+ 23.3452
Mo6+ 0.
Tc 86.8472
Ru 94.2928
Ru3+ 22.887
Ru4+ 20.8504
Rh 98.6062
Rh3+ -.01036
Rh4+ -.0102
Pd 76.8986
Pd2+ 0.
Pd4+ .005127
Ag 99.8156
Ag1+ 66.1147
Ag2+ 0.
Cd 87.4825
Cd2+ 0.
In 92.8029
In3+ 0.
Sn 83.9571
Sn2+ 62.2061
Sn4+ -.7583
Sb 75.2825
Sb3+ 55.5113
Sb5+ 0.
Te 70.8403
I 66.8776
I1- 84.9304
Xe 64.2658
Cs 213.904
Cs1+ 59.4565
Ba 167.202
Ba2+ 51.746
La 133.124
La3+ 54.9453
Ce 127.113
Ce3+ 43.1692
Ce4+ 62.2355
Pr 143.644
Pr3+ 36.4065
Pr4+ 45.4643
Nd 137.903
Nd3+ 30.8717
Pm 132.721
Sm 128.007
Sm3+ 24.8242
Eu 123.174
Eu2+ 26.5156
Eu3+ 22.9966
Gd 101.398
Gd3+ 21.7029
Tb 115.362
Tb3+ 21.2773
Dy 111.874
Dy3+ 19.581
Ho 92.6566
Ho3+ 18.5908
Er 105.703
Er3+ 17.8974
Tm 102.961
Tm3+ 17.2922
Yb 100.417
Yb2+ 20.39
Yb3+ 16.8153
Lu 84.3298
Lu3+ 16.3535
Hf 72.029
Hf4+ 14.0366
Ta 63.3644
Ta5+ 12.4244
W 57.056
W6+ 11.1972
Re 52.0861
Os 48.1647
Os4+ 18.003
Ir 45.0011
Ir3+ 20.3254
Ir4+ 17.4911
Pt 38.6103
Pt2+ 22.9426
Pt4+ 16.9392
Au 36.3956
Au1+ 26.4043
Au3+ 18.659
Hg 38.3246
Hg1+ 28.2262
Hg2+ 20.7482
Tl 45.8149
TL1+ 28.8482
Tl3+ 17.2114
Pb 47.2579
Pb2+ 23.8132
Pb4+ 14.714
Bi 48.0093
Bi3+ 20.3185
Bi5+ 12.8285
Po 47.0045
At 45.4715
Rn 44.2473
Fr 150.645
Ra 142.325
Ra2+ 29.8436
Ac 117.020
Ac3+ 25.9443
Th 99.1722
Th4+ 23.9533
Pa 105.251
U 100.613
U3+ 26.3394
U4+ 23.4582
U6+ 25.2017
Np 97.4908
Np3+ 25.4928
Np4+ 22.7502
Np6+ 22.6581
Pu 105.980
Pu3+ 24.3992
Pu4+ 21.8301
Pu6+ 20.9303
Am 102.273
Cm 88.4834
Bk 86.0030
Cf 83.7881
save_
save__atom_type_scat.Cromer_Mann_c
_definition.id '_atom_type_scat.Cromer_Mann_c'
loop_
_alias.definition_id
'_atom_type_scat.Cromer_Mann_c'
'_atom_type_scat_Cromer_Mann_c'
'_atom_type.scat_Cromer_Mann_c'
_name.category_id atom_type_scat
_name.object_id Cromer_Mann_c
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items used to define Cromer-Mann coefficients
for generation of X-ray scattering factors.
Ref: International Tables for X-ray Crystallography, Vol. IV
(1974) Table 2.2B
or International Tables for Crystallography, Vol. C
(1991) Tables 6.1.1.4 and 6.1.1.5
;
_enumeration.def_index_id '_atom_type.symbol'
_type.source Assigned
_type.container Single
_definition.update 2012-11-29
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H .003038
D .003038
H1- .002389
He 0.0064
Li .0377
Li1+ .0167
Be .0385
Be2+ -6.1092
B -.1932
C .2156
N -11.529
O .2508
O1- 21.9412
F .2776
F1- .653396
Ne 0.3515
Na .6760
Na1+ .4040
Mg .8584
Mg2+ .4853
Al 1.1151
Al3+ .706786
Si 1.1407
Si4+ .746297
P 1.1149
S .8669
Cl -9.5574
Cl1- -16.378
Ar 1.44450
K 1.4228
K1+ -4.9978
Ca 1.3751
Ca2+ -14.875
Sc 1.3329
Sc3+ -6.6667
Ti 1.2807
Ti2+ .897155
Ti3+ -14.652
Ti4+ -13.280
V 1.2199
V2+ 1.2298
V3+ .656565
V5+ 1.71430
Cr 1.1832
Cr2+ .616898
Cr3+ .518275
Mn 1.0896
Mn2+ 1.0874
Mn3+ .393974
Mn4+ .251877
Fe 1.0369
Fe2+ 1.0097
Fe3+ .9707
Co 1.0118
Co2+ .9324
Co3+ .286667
Ni 1.0341
Ni2+ .8614
Ni3+ .386044
Cu 1.1910
Cu1+ .8900
Cu2+ 1.14431
Zn 1.3041
Zn2+ .7807
Ga 1.7189
Ga3+ 1.53545
Ge 2.1313
Ge4+ 1.45572
As 2.5310
Se 2.8409
Br 2.9557
Br1- 3.1776
Kr 2.825
Rb 3.4873
Rb1+ 2.0782
Sr 2.5064
Sr2+ 41.4025
Y 1.91213
Y3+ 40.2602
Zr 2.06929
Zr4+ 9.41454
Nb 3.75591
Nb3+ -12.912
Nb5+ -6.3934
Mo 4.3875
Mo3+ -14.421
Mo5+ -14.316
Mo6+ .344941
Tc 5.40428
Ru 5.37874
Ru3+ -3.1892
Ru4+ 1.42357
Rh 5.32800
Rh3+ 11.8678
Rh4+ 11.2835
Pd 5.26593
Pd2+ 5.29160
Pd4+ 13.0174
Ag 5.1790
Ag1+ 5.21572
Ag2+ 5.21404
Cd 5.0694
Cd2+ 5.11937
In 4.9391
In3+ 4.99635
Sn 4.7821
Sn2+ 4.7861
Sn4+ 3.9182
Sb 4.5909
Sb3+ 4.69626
Sb5+ 4.69263
Te 4.35200
I 4.0712
I1- 4.0714
Xe 3.7118
Cs 3.3352
Cs1+ 3.2791
Ba 2.7731
Ba2+ 3.02902
La 2.14678
La3+ 2.40860
Ce 1.86264
Ce3+ 2.09013
Ce4+ 1.59180
Pr 2.05830
Pr3+ 1.77132
Pr4+ 1.24285
Nd 1.98486
Nd3+ 1.47588
Pm 2.02876
Sm 2.20963
Sm3+ .954586
Eu 2.5745
Eu2+ 1.36389
Eu3+ .759344
Gd 2.41960
Gd3+ .645089
Tb 3.58324
Tb3+ .691967
Dy 4.29728
Dy3+ .689690
Ho 4.56796
Ho3+ .852795
Er 5.92046
Er3+ 1.17613
Tm 6.75621
Tm3+ 1.63929
Yb 7.56672
Yb2+ 3.70983
Yb3+ 2.26001
Lu 7.97628
Lu3+ 2.97573
Hf 8.58154
Hf4+ 2.39699
Ta 9.24354
Ta5+ 1.78555
W 9.88750
W6+ 1.01074
Re 10.4720
Os 11.0005
Os4+ 6.49804
Ir 11.4722
Ir3+ 8.27903
Ir4+ 6.96824
Pt 11.6883
Pt2+ 9.85329
Pt4+ 7.39534
Au 12.0658
Au1+ 11.2299
Au3+ 9.09680
Hg 12.6089
Hg1+ 12.0205
Hg2+ 10.6268
Tl 13.1746
TL1+ 12.5258
Tl3+ 9.80270
Pb 13.4118
Pb2+ 12.4734
Pb4+ 8.08428
Bi 13.5782
Bi3+ 12.4711
Bi5+ -6.7994
Po 13.6770
At 13.7108
Rn 13.6905
Fr 13.7247
Ra 13.6211
Ra2+ 13.5431
Ac 13.5266
Ac3+ 13.4637
Th 13.4314
Th4+ 13.3760
Pa 13.4287
U 13.3966
U3+ 13.3092
U4+ 13.2671
U6+ 13.1665
Np 13.3573
Np3+ 13.2544
Np4+ 13.2116
Np6+ 13.1130
Pu 13.3812
Pu3+ 13.1991
Pu4+ 13.1555
Pu6+ 13.0582
Am 13.3592
Cm 13.2887
Bk 13.2754
Cf 13.2674
save_
save__atom_type_scat.Cromer_Mann_coeffs
_definition.id '_atom_type_scat.Cromer_Mann_coeffs'
loop_
_alias.definition_id
'_atom_type_scat.Cromer_Mann_coeffs'
_definition.update 2012-11-20
_description.text
;
The set of Cromer-Mann coefficients for generating X-ray scattering
factors. [ a1, b1, a2, b2, a3, b3, a4, b4, c]
Ref: International Tables for Crystallography, Vol. C
(1991) Table 6.1.1.4
;
_name.category_id atom_type_scat
_name.object_id Cromer_Mann_coeffs
_type.purpose Number
_type.source Derived
_type.container List
_type.contents Real
_type.dimension [9]
_units.code none
loop_
_method.purpose
_method.expression
Evaluation
;
With t as atom_type_scat
_atom_type_scat.Cromer_Mann_coeffs = [ t.Cromer_Mann_c,
t.Cromer_Mann_a1, t.Cromer_Mann_b1,
t.Cromer_Mann_a2, t.Cromer_Mann_b2,
t.Cromer_Mann_a3, t.Cromer_Mann_b3,
t.Cromer_Mann_a4, t.Cromer_Mann_b4 ]
;
save_
save__atom_type_scat.dispersion
_definition.id '_atom_type_scat.dispersion'
loop_
_alias.definition_id
'_atom_type_scat.dispersion'
_definition.update 2013-04-28
_description.text
;
The anomalous dispersion scattering factor in its complex form
for this atom type and radiation by _diffrn_radiation_wavelength.value
;
_name.category_id atom_type_scat
_name.object_id dispersion
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Complex
_enumeration.default 0.0
_units.code none
loop_
_method.purpose
_method.expression
Evaluation
;
With s as atom_type_scat
d = Complex( s.dispersion_real, s.dispersion_imag )
if(_reflns.apply_dispersion_to_Fcalc == 'no') d = 0.
_atom_type_scat.dispersion = d
;
save_
save__atom_type_scat.dispersion_imag
_definition.id '_atom_type_scat.dispersion_imag'
loop_
_alias.definition_id
'_atom_type_scat.dispersion_imag'
'_atom_type_scat_dispersion_imag'
'_atom_type.scat_dispersion_imag'
_definition.update 2012-11-20
_description.text
;
The imaginary component of the anomalous dispersion scattering factors
for this atom type and radiation by _diffrn_radiation_wavelength.value
;
_name.category_id atom_type_scat
_name.object_id dispersion_imag
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.default 0.0
_units.code none
loop_
_method.purpose
_method.expression
Evaluation
;
With q as atom_type_scat
If ( _diffrn_radiation.type[0:2] == 'Cu' ) a = q.dispersion_imag_cu
If ( _diffrn_radiation.type[0:2] == 'Mo' ) a = q.dispersion_imag_mo
_atom_type_scat.dispersion_imag = a
;
save_
save__atom_type_scat.dispersion_imag_cu
_definition.id '_atom_type_scat.dispersion_imag_cu'
loop_
_alias.definition_id
'_atom_type_scat.dispersion_imag_cu'
_definition.update 2012-11-20
_description.text
;
The imaginary component of the anomalous dispersion scattering factors
for this atom type and Cu K alpha radiation
;
_name.category_id atom_type_scat
_name.object_id dispersion_imag_cu
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.def_index_id '_atom_type.symbol'
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H .0
D .0
H1- .0
He .0
Li .0
Li1+ .0
Be .001
Be2+ .001
B .004
C .009
N .018
O .032
O1- .032
F .053
F1- .053
Ne .083
Na .124
Na1+ .124
Mg .177
Mg2+ .177
Al .246
Al3+ .246
Si .33
Si4+ .33
P .434
S .557
Cl .702
Cl1- .702
Ar .872
K 1.066
K1+ 1.066
Ca 1.286
Ca2+ 1.286
Sc 1.533
Sc3+ 1.533
Ti 1.807
Ti2+ 1.807
Ti3+ 1.807
Ti4+ 1.807
V 2.11
V2+ 2.11
V3+ 2.11
V5+ 2.11
Cr 2.443
Cr2+ 2.443
Cr3+ 2.443
Mn 2.808
Mn2+ 2.808
Mn3+ 2.808
Mn4+ 2.808
Fe 3.204
Fe2+ 3.204
Fe3+ 3.204
Co 3.608
Co2+ 3.608
Co3+ 3.608
Ni .509
Ni2+ .509
Ni3+ .509
Cu .589
Cu1+ .589
Cu2+ .589
Zn .678
Zn2+ .678
Ga 0.777
Ga3+ 0.777
Ge .886
Ge4+ .886
As 1.006
Se 1.139
Br 1.283
Br1- 1.283
Kr 1.439
Rb 1.608
Rb1+ 1.608
Sr 1.82
Sr2+ 1.82
Y 2.025
Y3+ 2.025
Zr 2.245
Zr4+ 2.245
Nb 2.482
Nb3+ 2.482
Nb5+ 2.482
Mo 2.735
Mo3+ 2.735
Mo5+ 2.735
Mo6+ 2.735
Tc 3.005
Ru 3.296
Ru3+ 3.296
Ru4+ 3.296
Rh 3.605
Rh3+ 3.605
Rh4+ 3.605
Pd 3.934
Pd2+ 3.934
Pd4+ 3.934
Ag 4.282
Ag1+ 4.282
Ag2+ 4.282
Cd 4.653
Cd2+ 4.653
In 5.045
In3+ 5.045
Sn 5.459
Sn2+ 5.459
Sn4+ 5.459
Sb 5.894
Sb3+ 5.894
Sb5+ 5.894
Te 6.352
I 6.835
I1- 6.835
Xe 7.348
Cs 7.904
Cs1+ 7.904
Ba 8.46
Ba2+ 8.46
La 9.036
La3+ 9.036
Ce 9.648
Ce3+ 9.648
Ce4+ 9.648
Pr 10.535
Pr3+ 10.535
Pr4+ 10.535
Nd 10.933
Nd3+ 10.933
Pm 11.614
Sm 12.32
Sm3+ 12.32
Eu 11.276
Eu2+ 11.276
Eu3+ 11.276
Gd 11.946
Gd3+ 11.946
Tb 9.242
Tb3+ 9.242
Dy 9.748
Dy3+ 9.748
Ho 3.704
Ho3+ 3.704
Er 3.937
Er3+ 3.937
Tm 4.181
Tm3+ 4.181
Yb 4.432
Yb2+ 4.432
Yb3+ 4.432
Lu 4.693
Lu3+ 4.693
Hf 4.977
Hf4+ 4.977
Ta 5.271
Ta5+ 5.271
W 5.577
W6+ 5.577
Re 5.891
Os 6.221
Os4+ 6.221
Ir 6.566
Ir3+ 6.566
Ir4+ 6.566
Pt 6.925
Pt2+ 6.925
Pt4+ 6.925
Au 7.297
Au1+ 7.297
Au3+ 7.297
Hg 7.686
Hg1+ 7.686
Hg2+ 7.686
Tl 8.089
TL1+ 8.089
Tl3+ 8.089
Pb 8.505
Pb2+ 8.505
Pb4+ 8.505
Bi 8.93
Bi3+ 8.93
Bi5+ 8.93
Po 9.383
At 9.843
Rn 10.317
Fr 10.803
Ra 11.296
Ra2+ 11.296
Ac 11.799
Ac3+ 11.799
Th 12.33
Th4+ 12.33
Pa 12.868
U 13.409
U3+ 13.409
U4+ 13.409
U6+ 13.409
Np 13.967
Np3+ 13.967
Np4+ 13.967
Np6+ 13.967
Pu 14.536
Pu3+ 14.536
Pu4+ 14.536
Pu6+ 14.536
Am 15.087
Cm 15.634
Bk 16.317
Cf 16.93
save_
save__atom_type_scat.dispersion_imag_mo
_definition.id '_atom_type_scat.dispersion_imag_mo'
loop_
_alias.definition_id
'_atom_type_scat.dispersion_imag_mo'
_definition.update 2012-11-20
_description.text
;
The imaginary component of the anomalous dispersion scattering factors
for this atom type and Mo K alpha radiation
;
_name.category_id atom_type_scat
_name.object_id dispersion_imag_mo
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.def_index_id '_atom_type.symbol'
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H .0
D .0
H1- .0
He .0
Li .0
Li1+ .0
Be .0
Be2+ .0
B .001
C .002
N .003
O .006
O1- .006
F .01
F1- .01
Ne .016
Na .025
Na1+ .025
Mg .036
Mg2+ .036
Al .052
Al3+ .052
Si .071
Si4+ .071
P .095
S .124
Cl .159
Cl1- .159
Ar .201
K .25
K1+ .25
Ca .306
Ca2+ .306
Sc 0.372
Sc3+ 0.372
Ti .446
Ti2+ .446
Ti3+ .446
Ti4+ .446
V .53
V2+ .53
V3+ .53
V5+ .53
Cr .624
Cr2+ .624
Cr3+ .624
Mn .729
Mn2+ .729
Mn3+ .729
Mn4+ .729
Fe .845
Fe2+ .845
Fe3+ .845
Co .973
Co2+ .973
Co3+ .973
Ni 1.113
Ni2+ 1.113
Ni3+ 1.113
Cu 1.266
Cu1+ 1.266
Cu2+ 1.266
Zn 1.431
Zn2+ 1.431
Ga 1.609
Ga3+ 1.609
Ge 1.801
Ge4+ 1.801
As 2.007
Se 2.223
Br 2.456
Br1- 2.456
Kr 2.713
Rb 2.973
Rb1+ 2.973
Sr 3.264
Sr2+ 3.264
Y 3.542
Y3+ 3.542
Zr .56
Zr4+ .56
Nb 0.621
Nb3+ 0.621
Nb5+ 0.621
Mo .688
Mo3+ .688
Mo5+ .688
Mo6+ .688
Tc .759
Ru .836
Ru3+ .836
Ru4+ .836
Rh .919
Rh3+ .919
Rh4+ .919
Pd 1.007
Pd2+ 1.007
Pd4+ 1.007
Ag 1.101
Ag1+ 1.101
Ag2+ 1.101
Cd 1.202
Cd2+ 1.202
In 1.31
In3+ 1.31
Sn 1.424
Sn2+ 1.424
Sn4+ 1.424
Sb 1.546
Sb3+ 1.546
Sb5+ 1.546
Te 1.675
I 1.812
I1- 1.812
Xe 1.958
Cs 2.119
Cs1+ 2.119
Ba 2.282
Ba2+ 2.282
La 2.452
La3+ 2.452
Ce 2.632
Ce3+ 2.632
Ce4+ 2.632
Pr 2.845
Pr3+ 2.845
Pr4+ 2.845
Nd 3.018
Nd3+ 3.018
Pm 3.225
Sm 3.442
Sm3+ 3.442
Eu 3.669
Eu2+ 3.669
Eu3+ 3.669
Gd 3.904
Gd3+ 3.904
Tb 4.151
Tb3+ 4.151
Dy 4.41
Dy3+ 4.41
Ho 4.678
Ho3+ 4.678
Er 4.958
Er3+ 4.958
Tm 5.248
Tm3+ 5.248
Yb 5.548
Yb2+ 5.548
Yb3+ 5.548
Lu 5.858
Lu3+ 5.858
Hf 6.185
Hf4+ 6.185
Ta 6.523
Ta5+ 6.523
W 6.872
W6+ 6.872
Re 7.232
Os 7.605
Os4+ 7.605
Ir 7.99
Ir3+ 7.99
Ir4+ 7.99
Pt 8.388
Pt2+ 8.388
Pt4+ 8.388
Au 8.798
Au1+ 8.798
Au3+ 8.798
Hg 9.223
Hg1+ 9.223
Hg2+ 9.223
Tl 9.659
TL1+ 9.659
Tl3+ 9.659
Pb 10.102
Pb2+ 10.102
Pb4+ 10.102
Bi 10.559
Bi3+ 10.559
Bi5+ 10.559
Po 11.042
At 9.961
Rn 10.403
Fr 7.754
Ra 8.105
Ra2+ 8.105
Ac 8.472
Ac3+ 8.472
Th 8.87
Th4+ 8.87
Pa 9.284
U 9.654
U3+ 9.654
U4+ 9.654
U6+ 9.654
Np 4.148
Np3+ 4.148
Np4+ 4.148
Np6+ 4.148
Pu 4.33
Pu3+ 4.33
Pu4+ 4.33
Pu6+ 4.33
Am 4.511
Cm 4.697
Bk 4.908
Cf 5.107
save_
save__atom_type_scat.dispersion_real
_definition.id '_atom_type_scat.dispersion_real'
loop_
_alias.definition_id
'_atom_type_scat.dispersion_real'
'_atom_type_scat_dispersion_real'
'_atom_type.scat_dispersion_real'
_definition.update 2012-11-20
_description.text
;
The real component of the anomalous dispersion scattering factors
for this atom type and radiation by _diffrn_radiation_wavelength.value
;
_name.category_id atom_type_scat
_name.object_id dispersion_real
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_units.code none
loop_
_method.purpose
_method.expression
Evaluation
;
With q as atom_type_scat
If ( _diffrn_radiation.type[0:2] == 'Cu' ) a = q.dispersion_real_cu
If ( _diffrn_radiation.type[0:2] == 'Mo' ) a = q.dispersion_real_mo
_atom_type_scat.dispersion_real = a
;
_enumeration.default 0.0
save_
save__atom_type_scat.dispersion_real_cu
_definition.id '_atom_type_scat.dispersion_real_cu'
loop_
_alias.definition_id
'_atom_type_scat.dispersion_real_cu'
_definition.update 2012-11-20
_description.text
;
The real component of the anomalous dispersion scattering factors
for this atom type and Cu K alpha radiation
;
_name.category_id atom_type_scat
_name.object_id dispersion_real_cu
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.def_index_id '_atom_type.symbol'
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H .0
D .0
H1- .0
He .0
Li .001
Li1+ .001
Be .003
Be2+ .003
B .008
C .017
N .029
O .047
O1- .047
F .069
F1- .069
Ne .097
Na 0.129
Na1+ 0.129
Mg .165
Mg2+ .165
Al .204
Al3+ .204
Si .244
Si4+ .244
P .283
S .319
Cl .348
Cl1- .348
Ar .366
K .365
K1+ .365
Ca .341
Ca2+ .341
Sc 0.285
Sc3+ 0.285
Ti .189
Ti2+ .189
Ti3+ .189
Ti4+ .189
V .035
V2+ .035
V3+ .035
V5+ .035
Cr -.198
Cr2+ -.198
Cr3+ -.198
Mn -.568
Mn2+ -.568
Mn3+ -.568
Mn4+ -.568
Fe -1.179
Fe2+ -1.179
Fe3+ -1.179
Co -2.464
Co2+ -2.464
Co3+ -2.464
Ni -2.956
Ni2+ -2.956
Ni3+ -2.956
Cu -2.019
Cu1+ -2.019
Cu2+ -2.019
Zn -1.612
Zn2+ -1.612
Ga -1.354
Ga3+ -1.354
Ge -1.163
Ge4+ -1.163
As -1.011
Se -.879
Br -.767
Br1- -.767
Kr -.665
Rb -.574
Rb1+ -.574
Sr -.465
Sr2+ -.465
Y -.386
Y3+ -.386
Zr -.314
Zr4+ -.314
Nb -.248
Nb3+ -.248
Nb5+ -.248
Mo -.191
Mo3+ -.191
Mo5+ -.191
Mo6+ -.191
Tc -.145
Ru -.105
Ru3+ -.105
Ru4+ -.105
Rh -.077
Rh3+ -.077
Rh4+ -.077
Pd -.059
Pd2+ -.059
Pd4+ -.059
Ag -.06
Ag1+ -.06
Ag2+ -.06
Cd -.079
Cd2+ -.079
In -.126
In3+ -.126
Sn -.194
Sn2+ -.194
Sn4+ -.194
Sb -.287
Sb3+ -.287
Sb5+ -.287
Te -.418
I -.579
I1- -.579
Xe -.783
Cs -1.022
Cs1+ -1.022
Ba -1.334
Ba2+ -1.334
La -1.716
La3+ -1.716
Ce -2.17
Ce3+ -2.17
Ce4+ -2.17
Pr -2.939
Pr3+ -2.939
Pr4+ -2.939
Nd -3.431
Nd3+ -3.431
Pm -4.357
Sm -5.696
Sm3+ -5.696
Eu -7.718
Eu2+ -7.718
Eu3+ -7.718
Gd -9.242
Gd3+ -9.242
Tb -9.498
Tb3+ -9.498
Dy -10.423
Dy3+ -10.423
Ho -12.255
Ho3+ -12.255
Er -9.733
Er3+ -9.733
Tm -8.488
Tm3+ -8.488
Yb -7.701
Yb2+ -7.701
Yb3+ -7.701
Lu -7.133
Lu3+ -7.133
Hf -6.715
Hf4+ -6.715
Ta -6.351
Ta5+ -6.351
W -6.048
W6+ -6.048
Re -5.79
Os -5.581
Os4+ -5.581
Ir -5.391
Ir3+ -5.391
Ir4+ -5.391
Pt -5.233
Pt2+ -5.233
Pt4+ -5.233
Au -5.096
Au1+ -5.096
Au3+ -5.096
Hg -4.99
Hg1+ -4.99
Hg2+ -4.99
Tl -4.883
TL1+ -4.883
Tl3+ -4.883
Pb -4.818
Pb2+ -4.818
Pb4+ -4.818
Bi -4.776
Bi3+ -4.776
Bi5+ -4.776
Po -4.756
At -4.772
Rn -4.787
Fr -4.833
Ra -4.898
Ra2+ -4.898
Ac -4.994
Ac3+ -4.994
Th -5.091
Th4+ -5.091
Pa -5.216
U -5.359
U3+ -5.359
U4+ -5.359
U6+ -5.359
Np -5.529
Np3+ -5.529
Np4+ -5.529
Np6+ -5.529
Pu -5.712
Pu3+ -5.712
Pu4+ -5.712
Pu6+ -5.712
Am -5.93
Cm -6.176
Bk -6.498
Cf -6.798
save_
save__atom_type_scat.dispersion_real_mo
_definition.id '_atom_type_scat.dispersion_real_mo'
loop_
_alias.definition_id
'_atom_type_scat.dispersion_real_mo'
_definition.update 2012-11-20
_description.text
;
The real component of the anomalous dispersion scattering factors
for this atom type and Mo K alpha radiation
;
_name.category_id atom_type_scat
_name.object_id dispersion_real_mo
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.def_index_id '_atom_type.symbol'
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H .0
D .0
H1- .0
He .0
Li .0
Li1+ .0
Be .0
Be2+ .0
B .0
C .002
N .004
O .008
O1- .008
F .014
F1- .014
Ne .021
Na 0.03
Na1+ 0.03
Mg .042
Mg2+ .042
Al .056
Al3+ .056
Si .072
Si4+ .072
P .09
S .11
Cl .132
Cl1- .132
Ar .155
K .179
K1+ .179
Ca .203
Ca2+ .203
Sc 0.226
Sc3+ 0.226
Ti .248
Ti2+ .248
Ti3+ .248
Ti4+ .248
V .267
V2+ .267
V3+ .267
V5+ .267
Cr .284
Cr2+ .284
Cr3+ .284
Mn .295
Mn2+ .295
Mn3+ .295
Mn4+ .295
Fe .301
Fe2+ .301
Fe3+ .301
Co .299
Co2+ .299
Co3+ .299
Ni .285
Ni2+ .285
Ni3+ .285
Cu .263
Cu1+ .263
Cu2+ .263
Zn .222
Zn2+ .222
Ga 0.163
Ga3+ 0.163
Ge .081
Ge4+ .081
As -.03
Se -.178
Br -.374
Br1- -.374
Kr -.652
Rb -1.044
Rb1+ -1.044
Sr -1.657
Sr2+ -1.657
Y -2.951
Y3+ -2.951
Zr -2.965
Zr4+ -2.965
Nb -2.197
Nb3+ -2.197
Nb5+ -2.197
Mo -1.825
Mo3+ -1.825
Mo5+ -1.825
Mo6+ -1.825
Tc -1.59
Ru -1.42
Ru3+ -1.42
Ru4+ -1.42
Rh -1.287
Rh3+ -1.287
Rh4+ -1.287
Pd -1.177
Pd2+ -1.177
Pd4+ -1.177
Ag -1.085
Ag1+ -1.085
Ag2+ -1.085
Cd -1.005
Cd2+ -1.005
In -.936
In3+ -.936
Sn -.873
Sn2+ -.873
Sn4+ -.873
Sb -.816
Sb3+ -.816
Sb5+ -.816
Te -.772
I -.726
I1- -.726
Xe -.684
Cs -.644
Cs1+ -.644
Ba -.613
Ba2+ -.613
La -.588
La3+ -.588
Ce -.564
Ce3+ -.564
Ce4+ -.564
Pr -.53
Pr3+ -.53
Pr4+ -.53
Nd -.535
Nd3+ -.535
Pm -.53
Sm -.533
Sm3+ -.533
Eu -.542
Eu2+ -.542
Eu3+ -.542
Gd -.564
Gd3+ -.564
Tb -.591
Tb3+ -.591
Dy -.619
Dy3+ -.619
Ho -.666
Ho3+ -.666
Er -.723
Er3+ -.723
Tm -.795
Tm3+ -.795
Yb -.884
Yb2+ -.884
Yb3+ -.884
Lu -.988
Lu3+ -.988
Hf -1.118
Hf4+ -1.118
Ta -1.258
Ta5+ -1.258
W -1.421
W6+ -1.421
Re -1.598
Os -1.816
Os4+ -1.816
Ir -2.066
Ir3+ -2.066
Ir4+ -2.066
Pt -2.352
Pt2+ -2.352
Pt4+ -2.352
Au -2.688
Au1+ -2.688
Au3+ -2.688
Hg -3.084
Hg1+ -3.084
Hg2+ -3.084
Tl -3.556
TL1+ -3.556
Tl3+ -3.556
Pb -4.133
Pb2+ -4.133
Pb4+ -4.133
Bi -4.861
Bi3+ -4.861
Bi5+ -4.861
Po -5.924
At -7.444
Rn -8.862
Fr -7.912
Ra -7.62
Ra2+ -7.62
Ac -7.725
Ac3+ -7.725
Th -8.127
Th4+ -8.127
Pa -8.96
U -10.673
U3+ -10.673
U4+ -10.673
U6+ -10.673
Np -11.158
Np3+ -11.158
Np4+ -11.158
Np6+ -11.158
Pu -9.725
Pu3+ -9.725
Pu4+ -9.725
Pu6+ -9.725
Am -8.926
Cm -8.416
Bk -7.99
Cf -7.683
save_
save__atom_type_scat.dispersion_source
_definition.id '_atom_type_scat.dispersion_source'
loop_
_alias.definition_id
'_atom_type_scat.dispersion_source'
'_atom_type_scat_dispersion_source'
'_atom_type.scat_dispersion_source'
_definition.update 2012-11-20
_description.text
;
Reference to source of real and imaginary dispersion
corrections for scattering factors used for this atom type.
;
_name.category_id atom_type_scat
_name.object_id dispersion_source
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'International Tables Vol. IV Table 2.3.1'
save_
save__atom_type_scat.hi_ang_Fox_c0
_definition.id '_atom_type_scat.hi_ang_Fox_c0'
loop_
_alias.definition_id
'_atom_type_scat.hi_ang_Fox_c0'
_name.category_id atom_type_scat
_name.object_id hi_ang_Fox_c0
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items used to define Fox et al. coefficients
for generation of high angle (s >2.0) X-ray scattering factors.
Ref: International Tables for Crystallography, Vol. C
(1991) Table 6.1.1.5
;
_enumeration.def_index_id '_atom_type.symbol'
_type.source Assigned
_type.container Single
_definition.update 2012-11-29
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H -4.8
D -4.8
H1- -4.8
He 0.52543
Li 0.89463
Li1+ 0.89463
Be 1.2584
Be2+ 1.2584
B 1.6672
C 1.70560
N 1.54940
O 1.30530
O1- 1.30530
F 1.16710
F1- 1.16710
Ne 1.09310
Na 0.84558
Na1+ 0.84558
Mg 0.71877
Mg2+ 0.71877
Al 0.67975
Al3+ 0.67975
Si 0.70683
Si4+ 0.70683
P 0.85532
S 1.10400
Cl 1.42320
Cl1- 1.42320
Ar 1.82020
K 2.26550
K1+ 2.26550
Ca 2.71740
Ca2+ 2.71740
Sc 3.11730
Sc3+ 3.11730
Ti 3.45360
Ti2+ 3.45360
Ti3+ 3.45360
Ti4+ 3.45360
V 3.71270
V2+ 3.71270
V3+ 3.71270
V5+ 3.71270
Cr 3.87870
Cr2+ 3.87870
Cr3+ 3.87870
Mn 3.98550
Mn2+ 3.98550
Mn3+ 3.98550
Mn4+ 3.98550
Fe 3.99790
Fe2+ 3.99790
Fe3+ 3.99790
Co 3.95900
Co2+ 3.95900
Co3+ 3.95900
Ni 3.86070
Ni2+ 3.86070
Ni3+ 3.86070
Cu 3.72510
Cu1+ 3.72510
Cu2+ 3.72510
Zn 3.55950
Zn2+ 3.55950
Ga 3.37560
Ga3+ 3.37560
Ge 3.17800
Ge4+ 3.17800
As 2.97740
Se 2.78340
Br 2.60610
Br1- 2.60610
Kr 2.44280
Rb 2.30990
Rb1+ 2.30990
Sr 2.21070
Sr2+ 2.21070
Y 2.14220
Y3+ 2.14220
Zr 2.12690
Zr4+ 2.12690
Nb 2.12120
Nb3+ 2.12120
Nb5+ 2.12120
Mo 2.18870
Mo3+ 2.18870
Mo5+ 2.18870
Mo6+ 2.18870
Tc 2.25730
Ru 2.37300
Ru3+ 2.37300
Ru4+ 2.37300
Rh 2.50990
Rh3+ 2.50990
Rh4+ 2.50990
Pd 2.67520
Pd2+ 2.67520
Pd4+ 2.67520
Ag 2.88690
Ag1+ 2.88690
Ag2+ 2.88690
Cd 3.08430
Cd2+ 3.08430
In 3.31400
In3+ 3.31400
Sn 3.49840
Sn2+ 3.49840
Sn4+ 3.49840
Sb 3.70410
Sb3+ 3.70410
Sb5+ 3.70410
Te 3.88240
I 4.08010
I1- 4.08010
Xe 4.24610
Cs 4.38910
Cs1+ 4.38910
Ba 4.51070
Ba2+ 4.51070
La 4.60250
La3+ 4.60250
Ce 4.69060
Ce3+ 4.69060
Ce4+ 4.69060
Pr 4.72150
Pr3+ 4.72150
Pr4+ 4.72150
Nd 4.75090
Nd3+ 4.75090
Pm 4.74070
Sm 4.71700
Sm3+ 4.71700
Eu 4.66940
Eu2+ 4.66940
Eu3+ 4.66940
Gd 4.61010
Gd3+ 4.61010
Tb 4.52550
Tb3+ 4.52550
Dy 4.45230
Dy3+ 4.45230
Ho 4.37660
Ho3+ 4.37660
Er 4.29460
Er3+ 4.29460
Tm 4.21330
Tm3+ 4.21330
Yb 4.13430
Yb2+ 4.13430
Yb3+ 4.13430
Lu 4.04230
Lu3+ 4.04230
Hf 3.95160
Hf4+ 3.95160
Ta 3.85000
Ta5+ 3.85000
W 3.76510
W6+ 3.76510
Re 3.67600
Os 3.60530
Os4+ 3.60530
Ir 3.53130
Ir3+ 3.53130
Ir4+ 3.53130
Pt 3.47070
Pt2+ 3.47070
Pt4+ 3.47070
Au 3.41630
Au1+ 3.41630
Au3+ 3.41630
Hg 3.37350
Hg1+ 3.37350
Hg2+ 3.37350
Tl 3.34590
TL1+ 3.34590
Tl3+ 3.34590
Pb 3.32330
Pb2+ 3.32330
Pb4+ 3.32330
Bi 3.31880
Bi3+ 3.31880
Bi5+ 3.31880
Po 3.32030
At 3.34250
Rn 3.37780
Fr 3.41990
Ra 3.47530
Ra2+ 3.47530
Ac 3.49020
Ac3+ 3.49020
Th 3.61060
Th4+ 3.61060
Pa 3.68630
U 3.76650
U3+ 3.76650
U4+ 3.76650
U6+ 3.76650
Np 3.82870
Np3+ 3.82870
Np4+ 3.82870
Np6+ 3.82870
Pu 3.88970
Pu3+ 3.88970
Pu4+ 3.88970
Pu6+ 3.88970
Am 3.95060
Cm 4.01470
Bk 4.07780
Cf 4.14210
save_
save__atom_type_scat.hi_ang_Fox_c1
_definition.id '_atom_type_scat.hi_ang_Fox_c1'
loop_
_alias.definition_id
'_atom_type_scat.hi_ang_Fox_c1'
_name.category_id atom_type_scat
_name.object_id hi_ang_Fox_c1
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items used to define Fox et al. coefficients
for generation of high angle (s >2.0) X-ray scattering factors.
Ref: International Tables for Crystallography, Vol. C
(1991) Table 6.1.1.5
;
_enumeration.def_index_id '_atom_type.symbol'
_type.source Assigned
_type.container Single
_definition.update 2012-11-29
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H -.5
D -.5
H1- -.5
He -3.433
Li -2.4366
Li1+ -2.4366
Be -1.9459
Be2+ -1.9459
B -1.8556
C -1.56760
N -1.20190
O -0.83742
O1- -0.83742
F -0.63203
F1- -0.63203
Ne -0.50221
Na -0.26294
Na1+ -0.26294
Mg -0.13144
Mg2+ -0.13144
Al -0.08756
Al3+ -0.08756
Si -0.09888
Si4+ -0.09888
P -0.21262
S -0.40325
Cl -0.63936
Cl1- -0.63936
Ar -0.92776
K -1.24530
K1+ -1.24530
Ca -1.55670
Ca2+ -1.55670
Sc -1.81380
Sc3+ -1.81380
Ti -2.01150
Ti2+ -2.01150
Ti3+ -2.01150
Ti4+ -2.01150
V -2.13920
V2+ -2.13920
V3+ -2.13920
V5+ -2.13920
Cr -2.19000
Cr2+ -2.19000
Cr3+ -2.19000
Mn -2.18850
Mn2+ -2.18850
Mn3+ -2.18850
Mn4+ -2.18850
Fe -2.11080
Fe2+ -2.11080
Fe3+ -2.11080
Co -1.99650
Co2+ -1.99650
Co3+ -1.99650
Ni -1.88690
Ni2+ -1.88690
Ni3+ -1.88690
Cu -1.65500
Cu1+ -1.65500
Cu2+ -1.65500
Zn -1.45100
Zn2+ -1.45100
Ga -1.23910
Ga3+ -1.23910
Ge -1.02230
Ge4+ -1.02230
As -0.81038
Se -0.61110
Br -0.43308
Br1- -0.43308
Kr -0.27244
Rb -0.14328
Rb1+ -0.14328
Sr -0.04770
Sr2+ -0.04770
Y 0.01935
Y3+ 0.01935
Zr 0.08618
Zr4+ 0.08618
Nb 0.05381
Nb3+ 0.05381
Nb5+ 0.05381
Mo -0.00655
Mo3+ -0.00655
Mo5+ -0.00655
Mo6+ -0.00655
Tc -0.05737
Ru -0.15040
Ru3+ -0.15040
Ru4+ -0.15040
Rh -0.25906
Rh3+ -0.25906
Rh4+ -0.25906
Pd -0.39137
Pd2+ -0.39137
Pd4+ -0.39137
Ag -0.56119
Ag1+ -0.56119
Ag2+ -0.56119
Cd -0.71450
Cd2+ -0.71450
In -0.89697
In3+ -0.89697
Sn -1.02990
Sn2+ -1.02990
Sn4+ -1.02990
Sb -1.18270
Sb3+ -1.18270
Sb5+ -1.18270
Te -1.30980
I -1.45080
I1- -1.45080
Xe -1.56330
Cs -1.65420
Cs1+ -1.65420
Ba -1.72570
Ba2+ -1.72570
La -1.77070
La3+ -1.77070
Ce -1.81790
Ce3+ -1.81790
Ce4+ -1.81790
Pr -1.81390
Pr3+ -1.81390
Pr4+ -1.81390
Nd -1.80800
Nd3+ -1.80800
Pm -1.76600
Sm -1.71410
Sm3+ -1.71410
Eu -1.64140
Eu2+ -1.64140
Eu3+ -1.64140
Gd -1.55750
Gd3+ -1.55750
Tb -1.45520
Tb3+ -1.45520
Dy -1.36440
Dy3+ -1.36440
Ho -1.27460
Ho3+ -1.27460
Er -1.18170
Er3+ -1.18170
Tm -1.09060
Tm3+ -1.09060
Yb -1.00310
Yb2+ -1.00310
Yb3+ -1.00310
Lu -0.90518
Lu3+ -0.90518
Hf -0.80978
Hf4+ -0.80978
Ta -0.70599
Ta5+ -0.70599
W -0.61807
W6+ -0.61807
Re -0.52688
Os -0.45420
Os4+ -0.45420
Ir -0.37856
Ir3+ -0.37856
Ir4+ -0.37856
Pt -0.31534
Pt2+ -0.31534
Pt4+ -0.31534
Au -0.25987
Au1+ -0.25987
Au3+ -0.25987
Hg -0.21428
Hg1+ -0.21428
Hg2+ -0.21428
Tl -0.18322
TL1+ -0.18322
Tl3+ -0.18322
Pb -0.15596
Pb2+ -0.15596
Pb4+ -0.15596
Bi -0.14554
Bi3+ -0.14554
Bi5+ -0.14554
Po -0.13999
At -0.15317
Rn -0.17800
Fr -0.20823
Ra -0.25005
Ra2+ -0.25005
Ac -0.25109
Ac3+ -0.25109
Th -0.35409
Th4+ -0.35409
Pa -0.41329
U -0.47542
U3+ -0.47542
U4+ -0.47542
U6+ -0.47542
Np -0.51955
Np3+ -0.51955
Np4+ -0.51955
Np6+ -0.51955
Pu -0.56296
Pu3+ -0.56296
Pu4+ -0.56296
Pu6+ -0.56296
Am -0.60554
Cm -0.65062
Bk -0.69476
Cf -0.73977
save_
save__atom_type_scat.hi_ang_Fox_c2
_definition.id '_atom_type_scat.hi_ang_Fox_c2'
loop_
_alias.definition_id
'_atom_type_scat.hi_ang_Fox_c2'
_name.category_id atom_type_scat
_name.object_id hi_ang_Fox_c2
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items used to define Fox et al. coefficients
for generation of high angle (s >2.0) X-ray scattering factors.
Ref: International Tables for Crystallography, Vol. C
(1991) Table 6.1.1.5
;
_enumeration.def_index_id '_atom_type.symbol'
_type.source Assigned
_type.container Single
_definition.update 2012-11-29
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H .0
D .0
H1- .0
He 4.8007
Li 2.325
Li1+ 2.325
Be 1.3046
Be2+ 1.3046
B 1.6044
C 1.18930
N 0.51064
O -0.16738
O1- -0.16738
F -0.40207
F1- -0.40207
Ne -0.53648
Na -0.87884
Na1+ -0.87884
Mg -1.20900
Mg2+ -1.20900
Al -0.95431
Al3+ -0.95431
Si -0.98356
Si4+ -0.98356
P -0.37390
S 0.20094
Cl 0.84722
Cl1- 0.84722
Ar 1.59220
K 2.38330
K1+ 2.38330
Ca 3.13170
Ca2+ 3.13170
Sc 3.71390
Sc3+ 3.71390
Ti 4.13170
Ti2+ 4.13170
Ti3+ 4.13170
Ti4+ 4.13170
V 4.35610
V2+ 4.35610
V3+ 4.35610
V5+ 4.35610
Cr 4.38670
Cr2+ 4.38670
Cr3+ 4.38670
Mn 4.27960
Mn2+ 4.27960
Mn3+ 4.27960
Mn4+ 4.27960
Fe 3.98170
Fe2+ 3.98170
Fe3+ 3.98170
Co 3.60630
Co2+ 3.60630
Co3+ 3.60630
Ni 3.12390
Ni2+ 3.12390
Ni3+ 3.12390
Cu 2.60290
Cu1+ 2.60290
Cu2+ 2.60290
Zn 2.03390
Zn2+ 2.03390
Ga 1.46160
Ga3+ 1.46160
Ge 0.89119
Ge4+ 0.89119
As 0.34861
Se -0.14731
Br -0.57381
Br1- -0.57381
Kr -0.95570
Rb -1.22600
Rb1+ -1.22600
Sr -1.41100
Sr2+ -1.41100
Y -1.52240
Y3+ -1.52240
Zr -1.49190
Zr4+ -1.49190
Nb -1.50070
Nb3+ -1.50070
Nb5+ -1.50070
Mo -1.25340
Mo3+ -1.25340
Mo5+ -1.25340
Mo6+ -1.25340
Tc -1.07450
Ru -0.77694
Ru3+ -0.77694
Ru4+ -0.77694
Rh -0.44719
Rh3+ -0.44719
Rh4+ -0.44719
Pd -0.05894
Pd2+ -0.05894
Pd4+ -0.05894
Ag 0.42189
Ag1+ 0.42189
Ag2+ 0.42189
Cd 0.84482
Cd2+ 0.84482
In 1.35030
In3+ 1.35030
Sn 1.68990
Sn2+ 1.68990
Sn4+ 1.68990
Sb 2.08920
Sb3+ 2.08920
Sb5+ 2.08920
Te 2.41170
I 2.76730
I1- 2.76730
Xe 3.04200
Cs 3.25450
Cs1+ 3.25450
Ba 3.41320
Ba2+ 3.41320
La 3.49970
La3+ 3.49970
Ce 3.60280
Ce3+ 3.60280
Ce4+ 3.60280
Pr 3.56480
Pr3+ 3.56480
Pr4+ 3.56480
Nd 3.51970
Nd3+ 3.51970
Pm 3.37430
Sm 3.20800
Sm3+ 3.20800
Eu 2.98580
Eu2+ 2.98580
Eu3+ 2.98580
Gd 2.73190
Gd3+ 2.73190
Tb 2.43770
Tb3+ 2.43770
Dy 2.17540
Dy3+ 2.17540
Ho 1.92540
Ho3+ 1.92540
Er 1.67060
Er3+ 1.67060
Tm 1.42390
Tm3+ 1.42390
Yb 1.18810
Yb2+ 1.18810
Yb3+ 1.18810
Lu 0.92889
Lu3+ 0.92889
Hf 0.67951
Hf4+ 0.67951
Ta 0.41103
Ta5+ 0.41103
W 0.18568
W6+ 0.18568
Re -0.04706
Os -0.22529
Os4+ -0.22529
Ir -0.41174
Ir3+ -0.41174
Ir4+ -0.41174
Pt -0.56487
Pt2+ -0.56487
Pt4+ -0.56487
Au -0.69030
Au1+ -0.69030
Au3+ -0.69030
Hg -0.79013
Hg1+ -0.79013
Hg2+ -0.79013
Tl -0.84911
TL1+ -0.84911
Tl3+ -0.84911
Pb -0.89878
Pb2+ -0.89878
Pb4+ -0.89878
Bi -0.90198
Bi3+ -0.90198
Bi5+ -0.90198
Po -0.89333
At -0.83350
Rn -0.74320
Fr -0.64000
Ra -0.50660
Ra2+ -0.50660
Ac -0.49651
Ac3+ -0.49651
Th -0.18926
Th4+ -0.18926
Pa -0.01192
U 0.16850
U3+ 0.16850
U4+ 0.16850
U6+ 0.16850
Np 0.29804
Np3+ 0.29804
Np4+ 0.29804
Np6+ 0.29804
Pu 0.42597
Pu3+ 0.42597
Pu4+ 0.42597
Pu6+ 0.42597
Am 0.54967
Cm 0.67922
Bk 0.80547
Cf 0.93342
save_
save__atom_type_scat.hi_ang_Fox_c3
_definition.id '_atom_type_scat.hi_ang_Fox_c3'
loop_
_alias.definition_id
'_atom_type_scat.hi_ang_Fox_c3'
_name.category_id atom_type_scat
_name.object_id hi_ang_Fox_c3
_type.contents Real
_type.purpose Number
_description.text
;
The set of data items used to define Fox et al. coefficients
for generation of high angle (s >2.0) X-ray scattering factors.
Ref: International Tables for Crystallography, Vol. C
(1991) Table 6.1.1.5
;
_enumeration.def_index_id '_atom_type.symbol'
_type.source Assigned
_type.container Single
_definition.update 2012-11-29
_units.code none
loop_
_enumeration_default.index
_enumeration_default.value
H .0
D .0
H1- .0
He -2.5476
Li -.71949
Li1+ -.71949
Be -0.04297
Be2+ -0.04297
B -0.65981
C -0.42715
N 0.02472
O 0.47500
O1- 0.47500
F 0.54352
F1- 0.54352
Ne 0.60957
Na 0.76974
Na1+ 0.76974
Mg 0.82738
Mg2+ 0.82738
Al 0.72294
Al3+ 0.72294
Si 0.55631
Si4+ 0.55631
P 0.20731
S -0.26058
Cl -0.76135
Cl1- -0.76135
Ar -1.32510
K -1.91290
K1+ -1.91290
Ca -2.45670
Ca2+ -2.45670
Sc -2.85330
Sc3+ -2.85330
Ti -3.11710
Ti2+ -3.11710
Ti3+ -3.11710
Ti4+ -3.11710
V -3.22040
V2+ -3.22040
V3+ -3.22040
V5+ -3.22040
Cr -3.17520
Cr2+ -3.17520
Cr3+ -3.17520
Mn -3.02150
Mn2+ -3.02150
Mn3+ -3.02150
Mn4+ -3.02150
Fe -2.71990
Fe2+ -2.71990
Fe3+ -2.71990
Co -2.37050
Co2+ -2.37050
Co3+ -2.37050
Ni -1.94290
Ni2+ -1.94290
Ni3+ -1.94290
Cu -1.49760
Cu1+ -1.49760
Cu2+ -1.49760
Zn -1.02160
Zn2+ -1.02160
Ga -0.55471
Ga3+ -0.55471
Ge -0.09984
Ge4+ -0.09984
As 0.32231
Se 0.69837
Br 1.00950
Br1- 1.00950
Kr 1.27070
Rb 1.45320
Rb1+ 1.45320
Sr 1.55410
Sr2+ 1.55410
Y 1.59630
Y3+ 1.59630
Zr 1.51820
Zr4+ 1.51820
Nb 1.50150
Nb3+ 1.50150
Nb5+ 1.50150
Mo 1.24010
Mo3+ 1.24010
Mo5+ 1.24010
Mo6+ 1.24010
Tc 1.06630
Ru 0.79060
Ru3+ 0.79060
Ru4+ 0.79060
Rh 0.49443
Rh3+ 0.49443
Rh4+ 0.49443
Pd 0.15404
Pd2+ 0.15404
Pd4+ 0.15404
Ag -0.25659
Ag1+ -0.25659
Ag2+ -0.25659
Cd -0.60990
Cd2+ -0.60990
In -1.03910
In3+ -1.03910
Sn -1.29860
Sn2+ -1.29860
Sn4+ -1.29860
Sb -1.61640
Sb3+ -1.61640
Sb5+ -1.61640
Te -1.86420
I -2.13920
I1- -2.13920
Xe -2.34290
Cs -2.49220
Cs1+ -2.49220
Ba -2.59590
Ba2+ -2.59590
La -2.64050
La3+ -2.64050
Ce -2.70670
Ce3+ -2.70670
Ce4+ -2.70670
Pr -2.65180
Pr3+ -2.65180
Pr4+ -2.65180
Nd -2.59010
Nd3+ -2.59010
Pm -2.44210
Sm -2.28170
Sm3+ -2.28170
Eu -2.07460
Eu2+ -2.07460
Eu3+ -2.07460
Gd -1.84040
Gd3+ -1.84040
Tb -1.57950
Tb3+ -1.57950
Dy -1.34550
Dy3+ -1.34550
Ho -1.13090
Ho3+ -1.13090
Er -0.91467
Er3+ -0.91467
Tm -0.70804
Tm3+ -0.70804
Yb -0.51120
Yb2+ -0.51120
Yb3+ -0.51120
Lu -0.29820
Lu3+ -0.29820
Hf -0.09620
Hf4+ -0.09620
Ta 0.11842
Ta5+ 0.11842
W 0.29787
W6+ 0.29787
Re 0.48180
Os 0.61700
Os4+ 0.61700
Ir 0.75967
Ir3+ 0.75967
Ir4+ 0.75967
Pt 0.87492
Pt2+ 0.87492
Pt4+ 0.87492
Au 0.96224
Au1+ 0.96224
Au3+ 0.96224
Hg 1.02850
Hg1+ 1.02850
Hg2+ 1.02850
Tl 1.05970
TL1+ 1.05970
Tl3+ 1.05970
Pb 1.08380
Pb2+ 1.08380
Pb4+ 1.08380
Bi 1.06850
Bi3+ 1.06850
Bi5+ 1.06850
Po 1.04380
At 0.97641
Rn 0.88510
Fr 0.78354
Ra 0.65836
Ra2+ 0.65836
Ac 0.64340
Ac3+ 0.64340
Th 0.36849
Th4+ 0.36849
Pa 0.20878
U 0.05060
U3+ 0.05060
U4+ 0.05060
U6+ 0.05060
Np -0.06566
Np3+ -0.06566
Np4+ -0.06566
Np6+ -0.06566
Pu -0.18080
Pu3+ -0.18080
Pu4+ -0.18080
Pu6+ -0.18080
Am -0.29112
Cm -0.40588
Bk -0.51729
Cf -0.62981
save_
save__atom_type_scat.hi_ang_Fox_coeffs
_definition.id '_atom_type_scat.hi_ang_Fox_coeffs'
loop_
_alias.definition_id
'_atom_type_scat.hi_ang_Fox_coeffs'
_definition.update 2012-11-30
_description.text
;
The set of Fox et al. coefficients for generating high angle
X-ray scattering factors. [ c0, c1, c2, c3 ]
Ref: International Tables for Crystallography, Vol. C
(1991) Table 6.1.1.5
;
_name.category_id atom_type_scat
_name.object_id hi_ang_Fox_coeffs
_type.purpose Number
_type.source Derived
_type.container List
_type.contents Real
_type.dimension [4]
_units.code none
loop_
_method.purpose
_method.expression
Evaluation
;
With t as atom_type_scat
_atom_type_scat.hi_ang_Fox_coeffs = \
[t.hi_ang_Fox_c0,t.hi_ang_Fox_c1,t.hi_ang_Fox_c2,t.hi_ang_Fox_c3]
;
save_
save__atom_type_scat.key
_definition.id '_atom_type_scat.key'
loop_
_alias.definition_id
'_atom_type_scat.key'
_definition.update 2012-11-20
_description.text
;
Value is a unique key to a set of ATOM_TYPE_SCAT items in a
looped list. This list may be joined with the ATOM_TYPE list.
;
_name.category_id atom_type_scat
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _atom_type_scat.key = _atom_type_scat.symbol'
save_
save__atom_type_scat.length_neutron
_definition.id '_atom_type_scat.length_neutron'
loop_
_alias.definition_id
'_atom_type_scat.length_neutron'
'_atom_type_scat_length_neutron'
'_atom_type.scat_length_neutron'
_definition.update 2012-11-20
_description.text
;
The bound coherent scattering length for the atom type at the
isotopic composition used for the diffraction experiment.
;
_name.category_id atom_type_scat
_name.object_id length_neutron
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.default 0.0
_units.code femtometres
save_
save__atom_type_scat.source
_definition.id '_atom_type_scat.source'
loop_
_alias.definition_id
'_atom_type_scat.source'
'_atom_type_scat_source'
'_atom_type.scat_source'
_definition.update 2012-11-20
_description.text
;
Reference to source of scattering factors used for this atom type.
;
_name.category_id atom_type_scat
_name.object_id source
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'International Tables Vol. IV Table 2.4.6B'
save_
save__atom_type_scat.symbol
_definition.id '_atom_type_scat.symbol'
loop_
_alias.definition_id
'_atom_type_scat.symbol'
'_atom_type_scat_symbol'
_definition.update 2013-01-23
_description.text
;
The identity of the atom specie(s) representing this atom type.
See _atom_type.symbol for further details.
;
_name.category_id atom_type_scat
_name.object_id symbol
_name.linked_item_id '_atom_type.symbol'
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save__atom_type_scat.versus_stol_list
_definition.id '_atom_type_scat.versus_stol_list'
loop_
_alias.definition_id
'_atom_type_scat.versus_stol_list'
'_atom_type_scat_versus_stol_list'
'_atom_type.scat_versus_stol_list'
_definition.update 2013-04-17
_description.text
;
List of scattering factors as a function of sin theta on lambda.
List has the form ['<stol value>':'<scatfac>', ....] in
increments of 0.01, increasing from 0.0.
;
_name.category_id atom_type_scat
_name.object_id versus_stol_list
_type.purpose Number
_type.source Assigned
_type.container List
_type.contents 'List(Real,Real)'
_type.dimension []
_units.code none
save_
save_REFINE
_definition.id REFINE
_definition.scope Category
_definition.class Set
_definition.update 2012-11-20
_description.text
;
The CATEGORY of data items used to specify information about the
refinement of the structural model.
;
_name.category_id STRUCTURE
_name.object_id REFINE
save_
save__refine.special_details
_definition.id '_refine.special_details'
loop_
_alias.definition_id
'_refine.special_details'
'_refine_special_details'
'_refine.details'
_definition.update 2012-11-20
_description.text
;
Details of the refinement not specified by other data items.
;
_name.category_id refine
_name.object_id special_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_REFINE_DIFF
_definition.id REFINE_DIFF
_definition.scope Category
_definition.class Set
_definition.update 2012-11-20
_description.text
;
The CATEGORY of data items which specify the electron density limits
in a difference Fourier map after the structure has been refined. The
rms value is with respect to the arithmetic mean density, and is derived
from summations over each grid point in the asymmetric unit of the cell.
;
_name.category_id REFINE
_name.object_id REFINE_DIFF
save_
save__refine_diff.density_max
_definition.id '_refine_diff.density_max'
loop_
_alias.definition_id
'_refine_diff.density_max'
'_refine_diff_density_max'
'_refine.diff_density_max'
_definition.update 2012-11-20
_description.text
;
Maximum density value in a difference Fourier map.
;
_name.category_id refine_diff
_name.object_id density_max
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range -100.:
loop_
_method.purpose
_method.expression
Definition
;
If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres"
Else If (_diffrn_radiation.probe == "electron") _units.code = "volts"
Else _units.code = "electrons"
;
save_
save__refine_diff.density_max_su
_definition.id '_refine_diff.density_max_su'
loop_
_alias.definition_id
'_refine_diff.density_max_su'
'_refine_diff_density_max_su'
'_refine.diff_density_max_esd'
_definition.update 2012-11-20
_description.text
;
Standard Uncertainty of the
Maximum density value in a difference Fourier map.
;
_name.category_id refine_diff
_name.object_id density_max_su
_name.linked_item_id '_refine_diff.density_max'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
save_
save__refine_diff.density_min
_definition.id '_refine_diff.density_min'
loop_
_alias.definition_id
'_refine_diff.density_min'
'_refine_diff_density_min'
'_refine.diff_density_min'
_definition.update 2012-11-20
_description.text
;
Miniumum density value in a difference Fourier map.
;
_name.category_id refine_diff
_name.object_id density_min
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range :100.
loop_
_method.purpose
_method.expression
Definition
;
If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres"
Else If (_diffrn_radiation.probe == "electron") _units.code = "volts"
Else _units.code = "electrons"
;
save_
save__refine_diff.density_min_su
_definition.id '_refine_diff.density_min_su'
loop_
_alias.definition_id
'_refine_diff.density_min_su'
'_refine_diff_density_min_su'
'_refine.diff_density_min_esd'
_definition.update 2012-11-20
_description.text
;
Standard Uncertainty of the
Miniumum density value in a difference Fourier map.
;
_name.category_id refine_diff
_name.object_id density_min_su
_name.linked_item_id '_refine_diff.density_min'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
save_
save__refine_diff.density_rms
_definition.id '_refine_diff.density_rms'
loop_
_alias.definition_id
'_refine_diff.density_rms'
'_refine_diff_density_rms'
'_refine.diff_density_rms'
_definition.update 2012-11-20
_description.text
;
Root mean square density value in a difference Fourier map.
This value is measured with respect to the arithmetic mean
density and is derived from summations over each grid point
in the asymmetric unit of the cell. This quantity is useful
for assessing the significance of *_min and *_max values,
and also for defining suitable contour levels.
;
_name.category_id refine_diff
_name.object_id density_rms
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range -100.:100.
loop_
_method.purpose
_method.expression
Definition
;
If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres"
Else If (_diffrn_radiation.probe == "electron") _units.code = "volts"
Else _units.code = "electrons"
;
save_
save__refine_diff.density_rms_su
_definition.id '_refine_diff.density_rms_su'
loop_
_alias.definition_id
'_refine_diff.density_rms_su'
'_refine_diff_density_rms_su'
'_refine.diff_density_rms_esd'
_definition.update 2012-11-20
_description.text
;
Standard Uncertainty of the
Root mean square density value in a difference Fourier map.
;
_name.category_id refine_diff
_name.object_id density_rms_su
_name.linked_item_id '_refine_diff.density_rms'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
save_
save_REFINE_LS
_definition.id REFINE_LS
_definition.scope Category
_definition.class Set
_definition.update 2012-11-20
_description.text
;
The CATEGORY of data items used to specify information about the
refinement of the structural model.
;
_name.category_id REFINE
_name.object_id REFINE_LS
save_
save__refine_ls.abs_structure_details
_definition.id '_refine_ls.abs_structure_details'
loop_
_alias.definition_id
'_refine_ls.abs_structure_details'
'_refine_ls_abs_structure_details'
'_refine.ls_abs_structure_details'
_definition.update 2012-11-20
_description.text
;
Details on the absolute structure and how it was determined.
;
_name.category_id refine_ls
_name.object_id abs_structure_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__refine_ls.abs_structure_Flack
_definition.id '_refine_ls.abs_structure_Flack'
loop_
_alias.definition_id
'_refine_ls.abs_structure_Flack'
'_refine_ls_abs_structure_Flack'
'_refine.ls_abs_structure_Flack'
_definition.update 2012-11-20
_description.text
;
The measure of absolute structure as defined by Flack (1983).
For centrosymmetric structures, the only permitted value, if the
data name is present, is 'inapplicable', represented by '.' .
For noncentrosymmetric structures, the value must lie in the
99.97% Gaussian confidence interval -3u =< x =< 1 + 3u and a
standard uncertainty (e.s.d.) u must be supplied. The
_enumeration.range of 0.0:1.0 is correctly interpreted as
meaning (0.0 - 3u) =< x =< (1.0 + 3u).
Ref: Flack, H. D. (1983). Acta Cryst. A39, 876-881.
;
_name.category_id refine_ls
_name.object_id abs_structure_Flack
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:1.0
_units.code none
save_
save__refine_ls.abs_structure_Flack_su
_definition.id '_refine_ls.abs_structure_Flack_su'
loop_
_alias.definition_id
'_refine_ls.abs_structure_Flack_su'
'_refine_ls_abs_structure_Flack_su'
'_refine.ls_abs_structure_Flack_esd'
_definition.update 2012-11-20
_description.text
;
Standard Uncertainty of the
The measure of absolute structure as defined by Flack (1983).
;
_name.category_id refine_ls
_name.object_id abs_structure_Flack_su
_name.linked_item_id '_refine_ls.abs_structure_Flack'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
save_
save__refine_ls.abs_structure_Rogers
_definition.id '_refine_ls.abs_structure_Rogers'
loop_
_alias.definition_id
'_refine_ls.abs_structure_Rogers'
'_refine_ls_abs_structure_Rogers'
'_refine.ls_abs_structure_Rogers'
_definition.update 2012-11-20
_description.text
;
The measure of absolute structure as defined by Rogers (1981).
The value must lie in the 99.97% Gaussian confidence interval
-1 -3u =< \h =< 1 + 3u and a standard uncertainty (e.s.d.) u must
be supplied. The _enumeration.range of -1.0:1.0 is correctly
interpreted as meaning (-1.0 - 3u) =< \h =< (1.0 + 3u).
Ref: Rogers, D. (1981). Acta Cryst. A37, 734-741.
;
_name.category_id refine_ls
_name.object_id abs_structure_Rogers
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range -1.0:1.0
_units.code none
save_
save__refine_ls.abs_structure_Rogers_su
_definition.id '_refine_ls.abs_structure_Rogers_su'
loop_
_alias.definition_id
'_refine_ls.abs_structure_Rogers_su'
'_refine_ls_abs_structure_Rogers_su'
'_refine.ls_abs_structure_Rogers_esd'
_definition.update 2012-11-20
_description.text
;
Standard Uncertainty of the
The measure of absolute structure as defined by Rogers (1981).
;
_name.category_id refine_ls
_name.object_id abs_structure_Rogers_su
_name.linked_item_id '_refine_ls.abs_structure_Rogers'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
save_
save__refine_ls.d_res_high
_definition.id '_refine_ls.d_res_high'
loop_
_alias.definition_id
'_refine_ls.d_res_high'
'_refine_ls_d_res_high'
'_refine.ls_d_res_high'
_definition.update 2012-11-20
_description.text
;
Highest resolution for the reflections used in refinement.
This corresponds to the smallest interpanar d value.
;
_name.category_id refine_ls
_name.object_id d_res_high
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__refine_ls.d_res_low
_definition.id '_refine_ls.d_res_low'
loop_
_alias.definition_id
'_refine_ls.d_res_low'
'_refine_ls_d_res_low'
'_refine.ls_d_res_low'
_definition.update 2012-11-20
_description.text
;
Lowest resolution for the reflections used in refinement.
This corresponds to the largest interpanar d value.
;
_name.category_id refine_ls
_name.object_id d_res_low
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__refine_ls.extinction_coef
_definition.id '_refine_ls.extinction_coef'
loop_
_alias.definition_id
'_refine_ls.extinction_coef'
'_refine_ls_extinction_coef'
'_refine.ls_extinction_coef'
_definition.update 2012-11-20
_description.text
;
The extinction coefficient used to calculate the correction
factor applied to the structure-factor data. The nature of the
extinction coefficient is given in the definitions of
_refine_ls.extinction_expression and _refine_ls.extinction_method.
For the 'Zachariasen' method it is the r* value; for the
'Becker-Coppens type 1 isotropic' method it is the 'g' value.
For 'Becker-Coppens type 2 isotropic' corrections it is
the 'rho' value. Note that the magnitude of these values is
usually of the order of 10000.
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
129-147, 148-153.
Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.
Larson, A. C. (1967). Acta Cryst. 23, 664-665.
;
_name.category_id refine_ls
_name.object_id extinction_coef
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code none
loop_
_description_example.case
_description_example.detail
3472(52) 'Zachariasen coefficient r* = 0.347(5)e+04'
save_
save__refine_ls.extinction_coef_su
_definition.id '_refine_ls.extinction_coef_su'
loop_
_alias.definition_id
'_refine_ls.extinction_coef_su'
'_refine_ls_extinction_coef_su'
'_refine.ls_extinction_coef_esd'
_definition.update 2012-11-20
_description.text
;
Standard Uncertainty of the extinction coefficient
;
_name.category_id refine_ls
_name.object_id extinction_coef_su
_name.linked_item_id '_refine_ls.extinction_coef'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code none
save_
save__refine_ls.extinction_expression
_definition.id '_refine_ls.extinction_expression'
loop_
_alias.definition_id
'_refine_ls.extinction_expression'
'_refine_ls_extinction_expression'
'_refine.ls_extinction_expression'
_definition.update 2012-11-20
_description.text
;
Description of or reference to the extinction-correction equation
used to apply the data item _refine_ls.extinction_coef. This
information should be sufficient to reproduce the extinction-
correction factors applied to the structure factors.
;
_name.category_id refine_ls
_name.object_id extinction_expression
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
_description_example.detail
'Larson approach'
; Larson, A. C. (1970). "Crystallographic Computing", edited by
F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard.
;
save_
save__refine_ls.extinction_method
_definition.id '_refine_ls.extinction_method'
loop_
_alias.definition_id
'_refine_ls.extinction_method'
'_refine_ls_extinction_method'
'_refine.ls_extinction_method'
_definition.update 2012-11-20
_description.text
;
Description of the extinction correction method applied with the
data item _refine_ls.extinction_coef. This description should
include information about the correction method, either 'Becker-
Coppens' or 'Zachariasen'. The latter is sometimes referred to as
the 'Larson' method even though it employs Zachariasen's formula.
The Becker-Coppens procedure is referred to as 'type 1' when
correcting secondary extinction dominated by the mosaic spread;
as 'type 2' when secondary extinction is dominated by particle
size and includes a primary extinction component; and as 'mixed'
when there are types 1 and 2.
For the Becker-Coppens method it is also necessary to set the
mosaic distribution as either 'Gaussian' or 'Lorentzian'; and the
nature of the extinction as 'isotropic' or 'anisotropic'. Note
that if either the 'mixed' or 'anisotropic' corrections are applied
the multiple coefficients cannot be contained in the
_refine_ls.extinction_coef and must be listed in *.special_details.
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-153.
Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.
Larson, A. C. (1967). Acta Cryst. 23, 664-665.
;
_name.category_id refine_ls
_name.object_id extinction_method
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
Zachariasen
'B-C type 2 Gaussian isotropic'
save_
save__refine_ls.F_calc_details
_definition.id '_refine_ls.F_calc_details'
loop_
_alias.definition_id
'_refine_ls.F_calc_details'
'_refine_ls_F_calc_details'
_definition.update 2013-01-21
_description.text
;
Details concerning the evaluation of the structure factors
using the expression given in _refine_ls.F_calc_formula.
;
_name.category_id refine_ls
_name.object_id F_calc_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
'Gaussian integration using 16 points'
; Bessel functions expansion up to 5th
order. estimated accuracy of Bessel
function better than 0.001 electrons
;
save_
save__refine_ls.F_calc_formula
_definition.id '_refine_ls.F_calc_formula'
loop_
_alias.definition_id
'_refine_ls.F_calc_formula'
'_refine_ls_F_calc_formula'
_definition.update 2013-01-23
_description.text
;
Analytical expression used to calculate the structure factors.
;
_name.category_id refine_ls
_name.object_id F_calc_formula
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save__refine_ls.F_calc_precision
_definition.id '_refine_ls.F_calc_precision'
loop_
_alias.definition_id
'_refine_ls.F_calc_precision'
'_refine_ls_F_calc_precision'
_definition.update 2013-01-21
_description.text
;
Estimate of the precision resulting from the numerical
approximations made during the evaluation of the structure
factors using the expression _refine_ls.F_calc_formula
following the method outlined in _refine_ls.F_calc_details.
;
_name.category_id refine_ls
_name.object_id F_calc_precision
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
loop_
_method.purpose
_method.expression
Definition
;
If (_diffrn_radiation.probe == "neutron") _units.code = "femtometres"
Else If (_diffrn_radiation.probe == "electron") _units.code = "volts"
Else _units.code = "electrons"
;
save_
save__refine_ls.goodness_of_fit_all
_definition.id '_refine_ls.goodness_of_fit_all'
loop_
_alias.definition_id
'_refine_ls.goodness_of_fit_all'
'_refine_ls_goodness_of_fit_all'
'_refine.ls_goodness_of_fit_all'
_definition.update 2012-11-20
_description.text
;
Least-squares goodness-of-fit parameter S for all reflections after
the final cycle of refinement. Ideally, account should be taken of
parameters restrained in the least squares.
{ sum { w [ Y(meas) - Y(calc) ]^2^ } }^1/2^
S = { ------------------------------------ }
{ Nref - Nparam }
Y(meas) = the measured coefficients
(see _refine_ls.structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls.structure_factor_coef)
w = the least-squares reflection weight
[1/(u^2^)]
u = standard uncertainty
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
;
_name.category_id refine_ls
_name.object_id goodness_of_fit_all
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls.goodness_of_fit_all_su
_definition.id '_refine_ls.goodness_of_fit_all_su'
loop_
_alias.definition_id
'_refine_ls.goodness_of_fit_all_su'
'_refine_ls_goodness_of_fit_all_su'
'_refine.ls_goodness_of_fit_all_esd'
_definition.update 2012-11-20
_description.text
;
Standard Uncertainty of the Least-squares goodness-of-fit
parameter S for all reflections after the final cycle of refinement.
;
_name.category_id refine_ls
_name.object_id goodness_of_fit_all_su
_name.linked_item_id '_refine_ls.goodness_of_fit_all'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls.goodness_of_fit_gt
_definition.id '_refine_ls.goodness_of_fit_gt'
loop_
_alias.definition_id
'_refine_ls.goodness_of_fit_gt'
'_refine_ls_goodness_of_fit_gt'
'_refine_ls_goodness_of_fit_obs'
'_refine.ls_goodness_of_fit_obs'
'_refine.ls_goodness_of_fit_gt'
_definition.update 2012-11-20
_description.text
;
Least-squares goodness-of-fit parameter S for significantly
intense reflections, (i.e. 'observed' reflections with values
greater-than the threshold set in _reflns.threshold_expression),
after the final cycle. Ideally, account should be taken of
parameters restrained in the least-squares refinement.
{ sum { w [ Y(meas_gt) - Y(calc) ]^2^ } }^1/2^
S = { --------------------------------------- }
{ Nref - Nparam }
Y(meas_gt) = the 'observed' coefficients
(see _refine_ls.structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls.structure_factor_coef)
w = the least-squares reflection weight
[1/(u^2^)]
u = standard uncertainty
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
;
_name.category_id refine_ls
_name.object_id goodness_of_fit_gt
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls.goodness_of_fit_gt_su
_definition.id '_refine_ls.goodness_of_fit_gt_su'
loop_
_alias.definition_id
'_refine_ls.goodness_of_fit_gt_su'
'_refine_ls_goodness_of_fit_gt_su'
'_refine.ls_goodness_of_fit_gt_esd'
'_refine.ls_goodness_of_fit_obs_esd'
_definition.update 2012-11-20
_description.text
;
Standard Uncertainty of the Least-squares goodness-of-fit
parameter S for gt reflections after the final cycle of refinement.
;
_name.category_id refine_ls
_name.object_id goodness_of_fit_gt_su
_name.linked_item_id '_refine_ls.goodness_of_fit_gt'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls.goodness_of_fit_ref
_definition.id '_refine_ls.goodness_of_fit_ref'
loop_
_alias.definition_id
'_refine_ls.goodness_of_fit_ref'
'_refine_ls_goodness_of_fit_ref'
'_refine.ls_goodness_of_fit_ref'
_definition.update 2012-11-20
_description.text
;
Least-squares goodness-of-fit parameter S for those reflections
included in the final cycle of refinement. Account should be
taken of restrained parameters.
{ sum { w [ Y(meas) - Y(calc) ]^2^ } }^1/2^
S = { ------------------------------------ }
{ Nref - Nparam }
Y(meas) = the measured coefficients
(see _refine_ls.structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls.structure_factor_coef)
w = the least-squares reflection weight
[1/(u^2^)]
u = standard uncertainty
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
;
_name.category_id refine_ls
_name.object_id goodness_of_fit_ref
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls.hydrogen_treatment
_definition.id '_refine_ls.hydrogen_treatment'
loop_
_alias.definition_id
'_refine_ls.hydrogen_treatment'
'_refine_ls_hydrogen_treatment'
'_refine.ls_hydrogen_treatment'
_definition.update 2012-11-20
_description.text
;
Code identifying how hydrogen atoms were treated in the refinement.
;
_name.category_id refine_ls
_name.object_id hydrogen_treatment
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
refall 'refined all H-atom parameters'
refxyz 'refined H-atom coordinates only'
refU 'refined H-atom U'
s "only'"
noref 'no refinement of H-atom parameters'
constr 'H-atom parameters constrained'
hetero
;H-atom parameters constrained for H on C, all
H-atom parameters refined for H on heteroatoms
;
heteroxyz
;H-atom parameters constrained for H on C, refined
H-atom coordinates only for H on heteroatoms
;
heteroU
;H-atom parameters constrained for H on C, refined
H-atom U's only for H on heteroatoms
;
heteronoref
;H-atom parameters constrained for H on C, no
refinement of H-atom parameters for H on heteroatoms
;
hetero-mixed
;H-atom parameters constrained for H on C and some
heteroatoms, all H-atom parameters refined
for H on remaining heteroatoms
;
heteroxyz-mixed
;H-atom parameters constrained for H on C and some
heteroatoms, refined H-atom coordinates only
for H on remaining heteroatoms
;
heteroU-mixed
;H-atom parameters constrained for H on C and some
heteroatoms, refined H-atom U's only for H on
remaining heteroatoms
;
heteronoref-mixed
;H-atom parameters constrained for H on C and some
heteroatoms, no refinement of H-atom parameters
for H on remaining heteroatoms
;
mixed 'some constrained, some independent'
undef 'H-atom parameters not defined'
_enumeration.default undef
save_
save__refine_ls.matrix_type
_definition.id '_refine_ls.matrix_type'
loop_
_alias.definition_id
'_refine_ls.matrix_type'
'_refine_ls_matrix_type'
'_refine.ls_matrix_type'
_definition.update 2012-11-20
_description.text
;
Code identifying the matrix type used for least-squares derivatives.
;
_name.category_id refine_ls
_name.object_id matrix_type
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
full full
fullcycle 'full with fixed elements per cycle'
atomblock 'block diagonal per atom'
userblock 'user-defined blocks'
diagonal 'diagonal elements only'
sparse 'selected elements only'
_enumeration.default full
save_
save__refine_ls.number_constraints
_definition.id '_refine_ls.number_constraints'
loop_
_alias.definition_id
'_refine_ls.number_constraints'
'_refine_ls_number_constraints'
'_refine.ls_number_constraints'
_definition.update 2012-11-20
_description.text
;
Number of constrained (non-refined or dependent) parameters
in the least-squares process. These may be due to symmetry or any
other constraint process (e.g. rigid-body refinement). See also
_atom_site.constraints and _atom_site.refinement_flags. A general
description of constraints may appear in _refine.special_details.
;
_name.category_id refine_ls
_name.object_id number_constraints
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 0:
_enumeration.default 0
save_
save__refine_ls.number_parameters
_definition.id '_refine_ls.number_parameters'
loop_
_alias.definition_id
'_refine_ls.number_parameters'
'_refine_ls_number_parameters'
'_refine.ls_number_parameters'
_definition.update 2012-11-20
_description.text
;
Number of parameters refined in the least-squares process. If
possible this number should include the restrained parameters.
The restrained parameters are distinct from the constrained
parameters (where one or more parameters are linearly dependent
on the refined value of another). Least-squares restraints
often depend on geometry or energy considerations and this
makes their direct contribution to this number, and to the
goodness-of-fit calculation, difficult to assess.
;
_name.category_id refine_ls
_name.object_id number_parameters
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save__refine_ls.number_reflns
_definition.id '_refine_ls.number_reflns'
loop_
_alias.definition_id
'_refine_ls.number_reflns'
'_refine_ls_number_reflns'
'_refine.ls_number_reflns_all'
_definition.update 2012-11-20
_description.text
;
Number of unique reflections used in the least-squares refinement.
;
_name.category_id refine_ls
_name.object_id number_reflns
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 1:
save_
save__refine_ls.number_reflns_gt
_definition.id '_refine_ls.number_reflns_gt'
loop_
_alias.definition_id
'_refine_ls.number_reflns_gt'
'_refine_ls_number_reflns_gt'
'_refine.ls_number_reflns_obs'
_definition.update 2012-11-20
_description.text
;
The number of reflections that satisfy the resolution limits
established by _refine.ls_d_res_high and _refine.ls_d_res_low
and the observation limit established by
_reflns.observed_criterion.
;
_name.category_id refine_ls
_name.object_id number_reflns_gt
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 1:
save_
save__refine_ls.number_restraints
_definition.id '_refine_ls.number_restraints'
loop_
_alias.definition_id
'_refine_ls.number_restraints'
'_refine_ls_number_restraints'
'_refine.ls_number_restraints'
_definition.update 2012-11-20
_description.text
;
Number of restrained parameters in the least-squares refinement. These
parameters do not directly dependent on another refined parameter. Often
restrained parameters involve geometry or energy dependencies. See also
_atom_site.constraints and _atom_site.refinement_flags. A description
of refinement constraints may appear in _refine.special_details.
;
_name.category_id refine_ls
_name.object_id number_restraints
_type.purpose Number
_type.source Recorded
_type.container Single
_type.contents Count
_enumeration.range 0:
save_
save__refine_ls.R_factor_all
_definition.id '_refine_ls.R_factor_all'
loop_
_alias.definition_id
'_refine_ls.R_factor_all'
'_refine_ls_R_factor_all'
'_refine.ls_R_factor_all'
_definition.update 2014-04-17
_description.text
;
Residual factor for all reflections satisfying the resolution limits
specified by _refine_ls.d_res_high and _refine_ls.d_res_low. This is
the conventional R factor. See also wR factor definitions.
sum | F(meas) - F(calc) |
R = ------------------------
sum | F(meas) |
F(meas) = the measured structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the specified reflections
;
_name.category_id refine_ls
_name.object_id R_factor_all
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
loop_
_method.purpose
_method.expression
Evaluation
;
sumFdiff = 0.
sumFmeas = 0.
Loop r as refln {
sumFdiff += Abs(r.F_calc - r.F_meas)
sumFmeas += Abs(r.F_meas)
}
_refine_ls.R_factor_all = sumFdiff / sumFmeas
;
save_
save__refine_ls.R_factor_gt
_definition.id '_refine_ls.R_factor_gt'
loop_
_alias.definition_id
'_refine_ls.R_factor_gt'
'_refine_ls_R_factor_obs'
'_refine_ls_R_factor_gt'
'_refine.ls_R_factor_obs'
'_refine.ls_R_factor_gt'
_definition.update 2012-11-20
_description.text
;
Residual factor for the reflections judged significantly intense
(see _reflns.number_gt and _reflns.threshold_expression) and included
in the refinement. The reflections also satisfy the resolution limits
specified by _refine_ls.d_res_high and _refine_ls.d_res_low. This is
the conventional R factor.
sum | F(meas_gt) - F(calc) |
R = -----------------------------
sum | F(meas_gt) |
F(meas_gt) = the 'observed' structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the specified reflections
;
_name.category_id refine_ls
_name.object_id R_factor_gt
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls.R_Fsqd_factor
_definition.id '_refine_ls.R_Fsqd_factor'
loop_
_alias.definition_id
'_refine_ls.R_Fsqd_factor'
'_refine_ls_R_Fsqd_factor'
'_refine.ls_R_Fsqd_factor_obs'
_definition.update 2012-11-20
_description.text
;
Residual factor R(Fsqd), calculated on the squared amplitudes of the
measured and calculated structure factors, for significantly intense
reflections (satisfying _reflns.threshold_expression) and included in
the refinement. The reflections also satisfy the resolution limits
specified by _refine_ls.d_res_high and _refine_ls.d_res_low.
sum | F(meas_gt)^2^ - F(calc)^2^ |
R(Fsqd) = ------------------------------------
sum F(meas_gt)^2^
F(meas_gt)^2^ = squares of the 'observed' structure-factor
F(calc)^2^ = squares of the calculated structure-factor
and the sum is taken over the specified reflections
;
_name.category_id refine_ls
_name.object_id R_Fsqd_factor
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls.R_I_factor
_definition.id '_refine_ls.R_I_factor'
loop_
_alias.definition_id
'_refine_ls.R_I_factor'
'_refine_ls_R_I_factor'
'_refine.ls_R_I_factor_obs'
_definition.update 2012-11-20
_description.text
;
Residual factor R(I) for significantly intense reflections (satisfying
_reflns.threshold_expression) and included in the refinement. This is
most often calculated in Rietveld refinements of powder data, where it
is referred to as R~B~ or R~Bragg~.
sum | I(meas_gt) - I(calc) |
R(I) = -----------------------------
sum | I(meas_gt) |
I(meas_gt) = the net 'observed' intensities
I(calc) = the net calculated intensities
and the sum is taken over the specified reflections
;
_name.category_id refine_ls
_name.object_id R_I_factor
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls.restrained_S_all
_definition.id '_refine_ls.restrained_S_all'
loop_
_alias.definition_id
'_refine_ls.restrained_S_all'
'_refine_ls_restrained_S_all'
'_refine.ls_restrained_S_all'
_definition.update 2012-11-20
_description.text
;
Least-squares goodness-of-fit parameter S' for all reflections after
the final cycle of least squares. This parameter explicitly includes
the restraints applied in the least-squares process. See also
_refine_ls.goodness_of_fit_all definition.
{sum { w [ Y(meas) - Y(calc) ]^2^ } }^1/2^
{ + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } }
S' = { -------------------------------------------------- }
{ N~ref~ + N~restr~ - N~param~ }
Y(meas) = the measured coefficients
(see _refine_ls.structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls.structure_factor_coef)
w = the least-squares reflection weight
[1/square of standard uncertainty (e.s.d.)]
P(calc) = the calculated restraint values
P(targ) = the target restraint values
w~r~ = the restraint weight
N~ref~ = the number of reflections used in the refinement
(see _refine_ls.number_reflns)
N~restr~ = the number of restraints
(see _refine_ls.number_restraints)
N~param~ = the number of refined parameters
(see _refine_ls.number_parameters)
sum is taken over the specified reflections
sum~r~ is taken over the restraints
;
_name.category_id refine_ls
_name.object_id restrained_S_all
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls.restrained_S_gt
_definition.id '_refine_ls.restrained_S_gt'
loop_
_alias.definition_id
'_refine_ls.restrained_S_gt'
'_refine_ls_restrained_S_obs'
'_refine_ls_restrained_S_gt'
'_refine.ls_restrained_S_obs'
_definition.update 2012-11-20
_description.text
;
Least-squares goodness-of-fit parameter S' for significantly intense
reflections (satisfying _reflns.threshold_expression) after the final
cycle of least squares. This parameter explicitly includes the restraints
applied. The expression for S' is given in _refine_ls.restrained_S_all.
{sum { w [ Y(meas_gt) - Y(calc) ]^2^ } }^1/2^
{ + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } }
S' = { -------------------------------------------------- }
{ N~ref~ + N~restr~ - N~param~ }
Y(meas_gt) = the 'observed' coefficients
(see _refine_ls.structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls.structure_factor_coef)
w = the least-squares reflection weight
[1/square of standard uncertainty (e.s.d.)]
P(calc) = the calculated restraint values
P(targ) = the target restraint values
w~r~ = the restraint weight
N~ref~ = the number of reflections used in the refinement
(see _refine_ls.number_reflns)
N~restr~ = the number of restraints
(see _refine_ls.number_restraints)
N~param~ = the number of refined parameters
(see _refine_ls.number_parameters)
sum is taken over the specified reflections
sum~r~ is taken over the restraints
;
_name.category_id refine_ls
_name.object_id restrained_S_gt
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls.shift_over_su_max
_definition.id '_refine_ls.shift_over_su_max'
loop_
_alias.definition_id
'_refine_ls.shift_over_su_max'
'_refine_ls_shift_over_su_max'
'_refine.ls_shift_over_esd_max'
'_refine.ls_shift_over_su_max'
'_refine_ls_shift/su_max'
'_refine_ls_shift/esd_max'
_definition.update 2012-11-20
_description.text
;
The largest ratio of the final least-squares parameter shift
to the final standard uncertainty (s.u., formerly described
as estimated standard deviation, e.s.d.).
;
_name.category_id refine_ls
_name.object_id shift_over_su_max
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls.shift_over_su_max_lt
_definition.id '_refine_ls.shift_over_su_max_lt'
loop_
_alias.definition_id
'_refine_ls.shift_over_su_max_lt'
'_refine_ls_shift/su_max_lt'
'_refine.ls_shift_over_su_max_lt'
_definition.update 2012-12-11
_description.text
;
Upper limit for the largest ratio of the final l-s parameter
shift divided by the final standard uncertainty. This item is
used when the largest value of the shift divided by the final
standard uncertainty is too small to measure.
;
_name.category_id refine_ls
_name.object_id shift_over_su_max_lt
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls.shift_over_su_mean
_definition.id '_refine_ls.shift_over_su_mean'
loop_
_alias.definition_id
'_refine_ls.shift_over_su_mean'
'_refine_ls_shift_over_su_mean'
'_refine.ls_shift_over_esd_mean'
'_refine.ls_shift_over_su_mean'
'_refine_ls_shift/su_mean'
'_refine_ls_shift/esd_mean'
_definition.update 2012-11-20
_description.text
;
The average ratio of the final least-squares parameter shift
to the final standard uncertainty (s.u., formerly described
as estimated standard deviation, e.s.d.).
;
_name.category_id refine_ls
_name.object_id shift_over_su_mean
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls.shift_over_su_mean_lt
_definition.id '_refine_ls.shift_over_su_mean_lt'
loop_
_alias.definition_id
'_refine_ls.shift_over_su_mean_lt'
'_refine_ls_shift/su_mean_lt'
'_refine.ls_shift_over_su_mean_lt'
_definition.update 2012-12-11
_description.text
;
Upper limit for the average ratio of the final l-s parameter
shift divided by the final standard uncertainty. This item is
used when the average value of the shift divided by the final
standard uncertainty is too small to measure.
;
_name.category_id refine_ls
_name.object_id shift_over_su_mean_lt
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls.structure_factor_coef
_definition.id '_refine_ls.structure_factor_coef'
loop_
_alias.definition_id
'_refine_ls.structure_factor_coef'
'_refine_ls_structure_factor_coef'
'_refine.ls_structure_factor_coef'
_definition.update 2012-11-20
_description.text
;
Structure-factor coefficient used in the least-squares process.
;
_name.category_id refine_ls
_name.object_id structure_factor_coef
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
F 'structure factor magnitude'
Fsqd 'structure factor squared'
Inet 'net intensity'
_enumeration.default F
save_
save__refine_ls.weighting_details
_definition.id '_refine_ls.weighting_details'
loop_
_alias.definition_id
'_refine_ls.weighting_details'
'_refine_ls_weighting_details'
'_refine.ls_weighting_details'
_definition.update 2012-11-20
_description.text
;
Description of special aspects of the weighting scheme used in the
least-squares refinement. Used to describe the weighting when the
value of _refine_ls.weighting_scheme is specified as 'calc'.
;
_name.category_id refine_ls
_name.object_id weighting_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
loop_
_description_example.case
;
Sigdel model of Konnert-Hendrickson:
Sigdel = Afsig + Bfsig*(sin(\q)/\l - 1/6)
Afsig = 22.0, Bfsig = 150.0 at the beginning of refinement.
Afsig = 16.0, Bfsig = 60.0 at the end of refinement.
;
save_
save__refine_ls.weighting_scheme
_definition.id '_refine_ls.weighting_scheme'
loop_
_alias.definition_id
'_refine_ls.weighting_scheme'
'_refine_ls_weighting_scheme'
'_refine.ls_weighting_scheme'
_definition.update 2012-11-20
_description.text
;
General description of the weighting scheme used in the least-squares.
An enumerated code should be contained in this description.
;
_name.category_id refine_ls
_name.object_id weighting_scheme
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
sigma "based on measured s.u.'s"
unit 'unit or no weights applied'
calc 'calculated weights applied'
_enumeration.default sigma
save_
save__refine_ls.wR_factor_all
_definition.id '_refine_ls.wR_factor_all'
loop_
_alias.definition_id
'_refine_ls.wR_factor_all'
'_refine_ls_wR_factor_all'
'_refine.ls_wR_factor_all'
_definition.update 2012-11-20
_description.text
;
Weighted residual factors for all reflections satisfying the resolution
limits specified by _refine_ls.d_res_high and _refine_ls.d_res_low.
See also the _refine_ls.R_factor_all definition.
( sum w [ Y(meas) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(meas)^2^ )
Y(meas) = the measured amplitude _refine_ls.structure_factor_coef
Y(calc) = the calculated amplitude _refine_ls.structure_factor_coef
w = the least-squares weight
and the sum is taken over the specified reflections
;
_name.category_id refine_ls
_name.object_id wR_factor_all
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls.wR_factor_gt
_definition.id '_refine_ls.wR_factor_gt'
loop_
_alias.definition_id
'_refine_ls.wR_factor_gt'
'_refine_ls_wR_factor_obs'
'_refine.ls_wR_factor_obs'
'_refine_ls_wR_factor_gt'
_definition.update 2012-11-20
_description.text
;
Weighted residual factors for significantly intense reflections
(satisfying @reflns_threshold_expression) included in the refinement.
The reflections must also satisfy the resolution limits established by
_refine_ls.d_res_high and _refine_ls.d_res_low.
( sum w [ Y(meas_gt) - Y(calc) ]^2^ )^1/2^
wR = ( ---------------------------------- )
( sum w Y(meas_gt)^2^ )
Y(meas_gt) = the 'observed' amplitude _refine_ls.structure_factor_coef
Y(calc) = the calculated amplitude _refine_ls.structure_factor_coef
w = the least-squares weight
and the sum is taken over the specified reflections
;
_name.category_id refine_ls
_name.object_id wR_factor_gt
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls.wR_factor_ref
_definition.id '_refine_ls.wR_factor_ref'
loop_
_alias.definition_id
'_refine_ls.wR_factor_ref'
'_refine_ls_wR_factor_ref'
_definition.update 2012-11-20
_description.text
;
Weighted residual factors for reflections included in the refinement
which satisfy the limits specified by _refine_ls.d_res_high and
_refine_ls.d_res_low.
( sum w [ Y(meas) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(meas)^2^ )
Y(meas) = the measured amplitude _refine_ls.structure_factor_coef
Y(calc) = the calculated amplitude _refine_ls.structure_factor_coef
w = the least-squares weight
and the sum is taken over the specified reflections
;
_name.category_id refine_ls
_name.object_id wR_factor_ref
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save_REFINE_LS_CLASS
_definition.id REFINE_LS_CLASS
_definition.scope Category
_definition.class Loop
_definition.update 2013-09-08
_description.text
;
The CATEGORY of data items used to specify information about the
refinement of the structural model.
;
_name.category_id REFINE_LS
_name.object_id CLASS
_category.key_id '_refine_ls_class.key'
_category.key_list ['_refine_ls_class.code']
save_
save__refine_ls_class.code
_definition.id '_refine_ls_class.code'
loop_
_alias.definition_id
'_refine_ls_class.code'
'_refine_ls_class_code'
_definition.update 2012-11-20
_description.text
;
Code identifying a certain reflection class.
;
_name.category_id refine_ls_class
_name.object_id code
_name.linked_item_id '_reflns_class.code'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Code
loop_
_description_example.case
1
m1
s2
save_
save__refine_ls_class.d_res_high
_definition.id '_refine_ls_class.d_res_high'
loop_
_alias.definition_id
'_refine_ls_class.d_res_high'
'_refine_ls_class_d_res_high'
_definition.update 2012-11-20
_description.text
;
Highest resolution for the reflections in this class.
This corresponds to the smallest interpanar d value.
;
_name.category_id refine_ls_class
_name.object_id d_res_high
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__refine_ls_class.d_res_low
_definition.id '_refine_ls_class.d_res_low'
loop_
_alias.definition_id
'_refine_ls_class.d_res_low'
'_refine_ls_class_d_res_low'
_definition.update 2012-11-20
_description.text
;
Lowest resolution for the reflections in this class.
This corresponds to the largest interpanar d value.
;
_name.category_id refine_ls_class
_name.object_id d_res_low
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code angstroms
save_
save__refine_ls_class.key
_definition.id '_refine_ls_class.key'
loop_
_alias.definition_id
'_refine_ls_class.key'
_definition.update 2012-11-20
_description.text
;
Value is a unique key to a set of REFINE_LS_CLASS items
in a looped list.
;
_name.category_id refine_ls_class
_name.object_id key
_type.purpose Key
_type.source Related
_type.container Single
_type.contents Code
loop_
_method.purpose
_method.expression
Evaluation ' _refine_ls_class.key = _refine_ls_class.code'
save_
save__refine_ls_class.R_factor_all
_definition.id '_refine_ls_class.R_factor_all'
loop_
_alias.definition_id
'_refine_ls_class.R_factor_all'
'_refine_ls_class_R_factor_all'
_definition.update 2012-11-20
_description.text
;
Residual factor for reflections in this class included in the
refinement. See _refine_ls.R_factor_all definition for details.
;
_name.category_id refine_ls_class
_name.object_id R_factor_all
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls_class.R_factor_gt
_definition.id '_refine_ls_class.R_factor_gt'
loop_
_alias.definition_id
'_refine_ls_class.R_factor_gt'
'_refine_ls_class_R_factor_gt'
'_refine_ls_class_R_factor_obs'
_definition.update 2012-11-20
_description.text
;
Residual factor for the reflections in this class judged
significantly intense (see _reflns.threshold_expression) and
included in refinement. See _refine_ls.R_factor_gt for details.
;
_name.category_id refine_ls_class
_name.object_id R_factor_gt
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls_class.R_Fsqd_factor
_definition.id '_refine_ls_class.R_Fsqd_factor'
loop_
_alias.definition_id
'_refine_ls_class.R_Fsqd_factor'
'_refine_ls_class_R_Fsqd_factor'
_definition.update 2012-11-20
_description.text
;
Residual factor R(F^2^) for reflections in this class judged
significantly intense (see _reflns.threshold_expression) and
included in refinement. See _refine_ls.R_Fsqd_factor for details.
;
_name.category_id refine_ls_class
_name.object_id R_Fsqd_factor
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls_class.R_I_factor
_definition.id '_refine_ls_class.R_I_factor'
loop_
_alias.definition_id
'_refine_ls_class.R_I_factor'
'_refine_ls_class_R_I_factor'
_definition.update 2012-11-20
_description.text
;
Residual factor R(I) for reflections in this class judged
significantly intense (see _reflns.threshold_expression) and
included in refinement. See _refine_ls.R_I_factor for details.
;
_name.category_id refine_ls_class
_name.object_id R_I_factor
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
save__refine_ls_class.wR_factor_all
_definition.id '_refine_ls_class.wR_factor_all'
loop_
_alias.definition_id
'_refine_ls_class.wR_factor_all'
'_refine_ls_class_wR_factor_all'
_definition.update 2012-11-20
_description.text
;
Weight residual for all reflections in this class judged
significantly intense (see _reflns.threshold_expression) and
included in refinement. See _refine_ls.wR_factor_all for details.
;
_name.category_id refine_ls_class
_name.object_id wR_factor_all
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.0:
_units.code none
save_
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