Format: https://blends.debian.org/blends/1.1
Task: mx
Description: Macro Molecular diffraction
 This metapackage will install all MX diffraction software for X-ray
 photons-and-neutrons PAN.
Comment: Improve the description

Recommends: python3-mrcfile

Recommends: python3-cctbx

Recommends: python3-dials-data

Recommends: python3-extra-data

Suggests: coot
WNPP: 531904
Homepage: http://biop.ox.ac.uk/coot/
License: GPLv3 GPLv2+ LGPLv3
Vcs-Browser: https://salsa.debian.org/science-team/coot
Vcs-Git: https://salsa.debian.org/science-team/coot.git
Pkg-Description: Crystallographic Object-Oriented Toolkit

Suggests: edna
Homepage: http://www.edna-site.org
License: GPL3+ LGPL3+
Pkg-Description: Framework to build online data analysis programs

Suggests: nmoldyn
Homepage: http://dirac.cnrs-orleans.fr/plone/software/nmoldyn/
Vcs-Browser: https://salsa.debian.org/science-team/nmoldyn
Vcs-Git: https://salsa.debian.org/science-team/nmoldyn.git
Pkg-Description: ?

Suggests: phenix
Homepage: http://phenix-online.org
License: phenix
Pkg-Description: automated determination of macromolecular structures

Suggests: 3dna
Homepage: http://x3dna.org/
License: non-free
Pkg-Description: 3DNA is a versatile, integrated software system for
 the analysis, rebuilding and visualization of three-dimensional
 nucleic-acid-containing structures. The software is applicable not
 only to DNA (as the name 3DNA may imply), but also to complicated RNA
 structures and DNA-protein complexes. In 3DNA, structural analysis
 and model rebuilding are two sides of the same coin: the description
 of structure is rigorous and reversible, thus allowing for its exact
 reconstruction based on the derived parameters. 3DNA automatically
 detects all non-cannonical base pairs, base triplets and higher-order
 associations, and coaxially stacked helices; provides a comprehensive
 collection of fiber models of regular DNA and RNA helices; generates
 highly effective schematic presentations that reveal key features of
 nucleic-acid structures; performs undisturbed base mutations, and
 have facilities for the analysis of molecular dynamics simulation
 trajectories.
Comment: binary-only

Suggests: adxv
Homepage: http://www.scripps.edu/~arvai/adxv.html
License: non-free
Pkg-Description: The principal application of adxv is to display
 protein crystallography X-Ray diffraction data. The data may be
 displayed as a 2-D image, 3-D wire mesh or as integer pixel
 values. Data may be saved as either tiff or postscript files. Adxv
 will display data from most current detectors:
 .
   * ADSC ccd
   * Mar ccd
   * Mar image plate (old and new format)
   * Raxis II & IV
   * Fuji image plate
   * Crystallographic Binary Format (CBF)
   * XDS .pck files
   * European Data Format (EDF)
   * NUMPY (NPY)
   * Raw binary 8, 16, 32 & 64 bit integer data
Comment: binary-only

Suggests: aimless
Homepage: http://www.mrc-lmb.cam.ac.uk/harry/pre/aimless.html
License: ?
Pkg-Description: This program scales together multiple observations of
 reflections, and merges multiple observations into an average
 intensity: it is a successor program to SCALA
 .
 Various scaling
 models can be used. The scale factor is a function of the primary
 beam direction, either as a smooth function of Phi (the rotation
 angle ROT), or expressed as BATCH (image) number (deprecated). In
 addition, the scale may be a function of the secondary beam
 direction, acting principally as an absorption correction expanded as
 spherical harmonics. The secondary beam correction is related to the
 absorption anisotropy correction described by Blessing (Ref Blessing
 (1995) ).
 .
 The merging algorithm analyses the data for outliers, and gives
 detailed analyses. It generates a weighted mean of the observations
 of the same reflection, after rejecting the outliers.
 .
 The program does several passes through the data:
 .
   * initial estimate of the scales
   * first round scale refinement, using strong data using an I/sigma(I) cutoff
   * first round of outlier rejection
   * if both summation and profile-fitted intensity estimates are
      present (from Mosflm), then the cross-over point is determined
      between using profile-fitted for weak data and summation for
      strong data.
   * first analysis pass to refine the "corrections" to the standard deviation estimates
   * final round scale refinement, using strong data within limits on the normalised intensity |E|^2
   * final analysis pass to refine the "corrections" to the standard deviation estimates
   * final outlier rejections
   * a final pass to apply scales, analyse agreement & write the output
     file, usually with merged intensities, but alternatively as file
     with scaled but unmerged observations, with partials summed and
     outliers rejected, for each dataset
 .
 Anomalous scattering is ignored during the scale determination (I+ &
 I- observations are treated together), but the merged file always
 contains I+ & I-, even if the ANOMALOUS OFF command is
 used. Switching ANOMALOUS ON does affect the statistics and the
 outlier rejection (qv)

Suggests: albula
Homepage: http://www.dectris.ch/software_albula.html
License: ?
Pkg-Description: Dectris diffraction image viewer and analysis tool

Recommends: apbs

Suggests: aplx
Homepage: http://www.microapl.co.uk/apl
License: non-free
Remark: APL language is it really usefull ?
Pkg-Description: ?

Suggests: atsas
Homepage: http://www.embl-hamburg.de/biosaxs/software.html
License: ?
Remark: which part of the suite is used ?
Pkg-Description: ?

Recommends: autodock

Suggests: autoproc
Homepage: http://www.globalphasing.com/autoproc
License: ?
Pkg-Description: MX data processing
Remark: http://www.globalphasing.com/autoproc/licence/index.html ok for non-free ?
 needed: mosflm, scala, xds, pointless, ccp4, gnuplot

Recommends: openbabel

Suggests: balbes
Homepage: http://www.ysbl.york.ac.uk/~fei/balbes
License: ?
Pkg-Description: BALBES is a system for solving protein structures
 using x-ray crystallographic data. Molecular Replacement(MR) is its
 core scientific method. BALBES aims to integrate all components,
 necessary for finding a solution structure by MR, into one system. It
 consists of a database, scientific programs and a python
 pipeline. The system is automated so that it needs no user's
 intervention when running complicated combination of jobs such as
 model searching, molecular replacement and refinement.
 .
 F.Long, A.Vagin, P.Young and G.N.Murshudov "BALBES: a Molecular Replacement Pipeline " Acta Cryst. D64 125-132(2008)
Remark: need ccp4

Suggests: best
Homepage: http://www.embl-hamburg.de/BEST/
License: ?
Registration: http://www.embl-hamburg.de/BEST/download_request3.1.html
Pkg-Description: optimal planning of X-ray data collection from protein crystals

Suggests: bioxhit
Homepage: http://www.bioxhit.org
License: ?
Pkg-Description: ?
Remark: ESRF can you gives more information about this software

Suggests: biox-xds
Homepage: ?
License: ?
Pkg-Description: ?
Remark: ESRF can you gives more information about this software

Suggests: bobscript
Homepage: ?
License: ?
Pkg-Description: ?
Remark: ESRF can you gives more information about this software

Suggests: bp3-old
Homepage: ?
Remark: ESRF can you gives more information about this software
Pkg-Description: ?

Suggests: c3d
Homepage: ?
License: ?
Remark: ESRF can you gives more information about this software
Pkg-Description: ?

Suggests: cath
Homepage: http://www.cathdb.info
License: ?
Remark: used ?
Pkg-Description: CATH is a manually curated classification of protein
 domain structures. Each protein has been chopped into structural
 domains and assigned into homologous superfamilies (groups of domains
 that are related by evolution). This classification procedure uses a
 combination of automated and manual techniques which include
 computational algorithms, empirical and statistical evidence,
 literature review and expert analysis.

Suggests: ccp4
Homepage: http://www.ccp4.ac.uk
License: ?
Pkg-Description: CCP4 exists to produce and support a world-leading,
 integrated suite of programs that allows researchers to determine
 macromolecular structures by X-ray crystallography, and other
 biophysical techniques. CCP4 aims to develop and support the
 development of cutting edge approaches to experimental determination
 and analysis of protein structure, and integrate these approaches
 into the suite. CCP4 is a community based resource that supports the
 widest possible researcher community, embracing academic, not for
 profit, and for profit research. CCP4 aims to play a key role in the
 education and training of scientists in experimental structural
 biology. It encourages the wide dissemination of new ideas,
 techniques and practice.
Remark: this is a suite of software.

Suggests: cctbx
WNPP: 679905
Homepage: http://cctbx.sourceforge.net
Vcs-Browser: https://salsa.debian.org/science-team/cctbx
Vcs-Git: https://salsa.debian.org/science-team/cctbx.git
Pkg-Description: CCTBX is a toolbox for developing crystallographic
 software. It provides fundamental and advanced methods and algorithms
 usefull in the scientific fields of crystallography[1], chemistry,
 physics and biology. It also provides Libraries for general
 scientific computing.  The package is organized as a set of ISO C++
 classes with Python bindings.

Suggests: chart
Homepage: ?
License: ?
Pkg-Description: ?
Remark: ESRF can you gives more information about this software

Suggests: chimera
Homepage: http://www.cgl.ucsf.edu/chimera/
License: ?
Pkg-Description: UCSF Chimera is a highly extensible program for
 interactive visualization and analysis of molecular structures and
 related data, including density maps, supramolecular assemblies,
 sequence alignments, docking results, trajectories, and
 conformational ensembles. High-quality images and animations can be
 generated. Chimera includes complete documentation and several
 tutorials, and can be downloaded free of charge for academic,
 government, non-profit, and personal use. Chimera is developed by the
 Resource for Biocomputing, Visualization, and Informatics, funded by
 the National Institutes of Health National Center for Research
 Resources (grant 2P41RR001081) and National Institute of General
 Medical Sciences (grant 9P41GM103311).
Remark: binary only ?

Suggests: chooch
Homepage: http://www.gwyndafevans.co.uk/chooch.html
License: ?
Pkg-Description: CHOOCH is a program that will automatically determine
 values of the anomalous scattering factors, f' and f'', directly from
 experimentally measured X-ray fluorescence data. It outputs the f'
 and f'' spectrum and the appropriate X-ray wavelengths to be used for
 MAD or SAD experiments.
Remark: part of ccp4

Recommends: clustalw

Suggests: cn2coot
Homepage: ?
License: ?
Pkg-Description: ?
Remark: ESRF can you gives more information about this software

Suggests: cns
Homepage: http://cns.csb.yale.edu/v1.2/
License: non-free
Pkg-Description: Crystallography & NMR System (CNS) is the result of
 an international collaborative effort among several research
 groups. The program has been designed to provide a flexible
 multi-level hierachical approach for the most commonly used
 algorithms in macromolecular structure determination. Highlights
 include heavy atom searching, experimental phasing (including MAD and
 MIR), density modification, crystallographic refinement with maximum
 likelihood targets, and NMR structure calculation using NOEs,
 J-coupling, chemical shift, and dipolar coupling data.

Suggests: crank
Homepage: http://www.ccp4.ac.uk/html/crank.html
License: non-free
Pkg-Description: Crank [1] is a program to automate macromolecular
 structure determination for single or multiple-wavelength anomalous
 diffraction (SAD/MAD) or single isomorphous replacement (SIRAS)
 experiments. Crank interfaces with various crystallographic programs
 and is designed to allow both the automation of the structure
 determination process, but also allow the user to re-run and optmize
 results, if necessary.
 .
 This version of Crank has interfaces to the programs CRUNCH2 [2] and
 SHELXD [3] for substructure detection, BP3 [4], [5] for substructure
 phasing, SOLOMON [6], DM [7], SHELXE [8], PIRATE [9] and RESOLVE [23]
 for density modification and RESOLVE [24], BUCCANEER [25] and
 ARP/wARP [10] for automated model building. ARP/wARP uses REFMAC [11]
 for iterative refinement. Within REFMAC, either the likelihood
 function restraining phases via Hendrickson-Lattman coefficients [12]
 or a multivariate likelihood SAD function [13] is used. To calculate
 FA values needed for substructure detection, crank interfaces with
 the programs SHELXC [14] or AFRO [15]. For setting up and preparing
 files, crank using programs from the CCP4 [16] suite, including
 SFTOOLS [17] and TRUNCATE [18]. Also, crank uses the
 Kantardjieff-Rupp algorithm [19] which performs a probabilistic
 Matthew's coefficient [20] calculation for estimating the number of
 monomers in the asymmetric unit. To visualize the results produced by
 crank, an interface to COOT [26] is also available.
 .
 Crank can be run using its CCP4i [21] interface or via script using
 the program GCX [22]. Crank's only dependency to produce a density
 modified map is a licenced CCP4 version 5.99.x or later. If you would
 like to use the SHELX [13] programs, ARP/wARP [10], RESOLVE [23],
 [24] and/or BUCCANEER [25] within crank, you must have it installed
 on your system with the appropriate licence. If these programs do not
 appear in your path, they will not appear as options in the ccp4i
 interface.
Remark: You need a licenced version of CCP4 6.0 or higher installed to
 use crank and if you wish to use the ARP/wARP, RESOLVE and/or
 SHELX[C/D/E] software within crank, they also must be installed on
 your system, and you must comply with the software's licence
 agreement.

Suggests: crystfel
WNPP: 743268
Homepage: http://www.desy.de/~twhite/crystfel/
License: GPLv3+
Pkg-Description: CrystFEL is a suite of programs for processing
 diffraction data acquired "serially" in a "snapshot" manner. That
 means: a large number of individual diffraction patterns, each
 corresponding to a random orientation of the crystal, with little or
 no rotation or oscillation of the sample. This is exactly the
 situation encountered when using the technique of Serial Femtosecond
 Crystallography (SFX) with a free-electron laser source, which is the
 application CrystFEL is primarily designed for.
Remark: if you intent to package a software of this task, please
 considere this one.
Published-Authors: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman.
Published-Title: "CrystFEL: a software suite for snapshot serial crystallography".
Published-In: J. Appl. Cryst. 45, p335–341.
Published-DOI: 10.1107/S0021889812002312
Published-URL: http://www.desy.de/~twhite/crystfel/db5097-reprint.pdf

Suggests: das
Homepage: http://www.biodas.org/wiki/Main_Page
License: ?
Pkg-Description: The Distributed Annotation System (DAS) defines a
 communication protocol used to exchange annotations on genomic or
 protein sequences. It is motivated by the idea that such annotations
 should not be provided by single centralized databases, but should
 instead be spread over multiple sites. Data distribution, performed
 by DAS servers, is separated from visualization, which is done by DAS
 clients. The advantages of this system are that control over the data
 is retained by data providers, data is freed from the constraints of
 specific organisations and the normal issues of release cycles, API
 updates and data duplication are avoided.
 .
 DAS is a client-server system in which a single client integrates
 information from multiple servers. It allows a single machine to
 gather up sequence annotation information from multiple distant web
 sites, collate the information, and display it to the user in a
 single view. Little coordination is needed among the various
 information providers.
 .
 DAS is heavily used in the genome bioinformatics community. Over the
 last years we have also seen growing acceptance in the protein
 sequence and structure communities.
Remark: ESRF can you gives more information about this software

Suggests: dna
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?
Remark: ESRF can you gives more information about this software

Suggests: domain-finder
Homepage: http://dirac.cnrs-orleans.fr/DomainFinder/
License: GPLv3+
Pkg-Description: DomainFinder is an interactive program for the
 determination and characterization of dynamical domains in
 proteins. Its key features are
 .
   * computational efficiency: even large proteins can be analyzed
     using a desktop computer in a few minutes
   * ease of use: a state-of-the-art graphical user interface
   * export of results for visualization and further analysis (VRML,
     PDB, and MMTK object format)
 .
 Dynamical domains are an important concept in the description of
 protein dynamics. A dynamical domain is a region in a protein which
 can move essentially like a rigid body relative to other
 regions. Many, but not all, proteins have dynamical domains, and if
 they do, the relative movements of the domains are usually related to
 the function of the protein. The identification of dynamical domains
 is therefore useful in understanding the function of the
 protein. However, there are other situations in which the knowledge
 of dynamical domains is helpful. In structure determination, it can
 help to predict whether complexation with a ligand, crystal packing,
 or other external influences can lead to important conformational
 changes. In protein engineering, it can indicate whether a given
 modification is likely to change the dynamical behavior of the
 protein. In experimental observations of protein motion, it can
 suggest regions of particular interest. In numerical simulations, it
 can point out the slow motions whose correct sampling must be
 verified.
 .
 DomainFinder is written in Python, a high-level object programming
 language that is particularly well suited to the demands of
 scientific computations. The speed-critical parts are implemented in
 C. For common operations it makes use of the Molecular Modeling
 Toolkit, a library of Python code for molecular modelling and
 simulation applications. The results of a domain analysis can be
 saved with all details in an MMTK data file, which permits all kinds
 of further analysis.

Suggests: dps2ar
Homepage: http://www.embl-hamburg.de/Auto-Rickshaw/DPS2AR/
License: ?
Pkg-Description: The EMBL-Hamburg automated crystal structure
 determination platform is a system which contains several distinct
 decision-makers which utilize a number of macromolecular
 crystallographic software programs to produce a software pipeline for
 automated and efficient crystal structure determination. A large
 number of possible structure solution paths are encoded in the system
 and the optimal path is selected by the decision-makers as the
 structure solution evolves. The processes have been optimised for
 speed so that the pipeline can be used effectively for validating the
 X-ray experiment at a synchrotron beamline. Currently, the platform
 offers SAD, SIRAS, 2W-MAD, 3W-MAD or 4W-MAD phase determination,
 molecular replacement (MR) and MRSAD phasing. Recently it has been
 extended to include RIP and MRRIP phasing.
 .
 Auto-Rickshaw comes in two flavours : a Beamline Version and an
 Advanced Version. Both versions use a similar GUI for input, but the
 Advanced Version requires the sequence information for the protein
 target in order to build the side chains.
 .
 The “Beamline Version” is explicitly designed for use in validation
 of the X-ray experiment at the synchrotron beamline as soon as the
 data have been collected and processed.  Once the X-ray experiment is
 validated, the “Advanced Version” can be used for a more complete
 model building if the resolution of the data permits. The “Advanced
 Version” of the platform uses ARP/wARP, beta-version of SHELXE,
 RESOLVE and BUCCANEER
 .
 The Auto-Rickshaw platform has been installed on a 64-processors
 Linux cluster and is remotely accessible to academic users via a
 web-server . It allows to evaluate the success of their X-ray
 diffraction experiments in the shortest possible time. This helps to
 ensure an efficient use of the beam time available. The platform is
 undergoing continuous development. This includes the improvement of
 the platform's decision makers, the incorporation of new
 functionalities as well as continuous software upgrades. An
 emulation of the Auto-Rickshaw job submission.
 .
 Auto-Rickshaw server is freely accessible to users at academic
 institution upon online registration .

Suggests: dviewer
Homepage: ?
License: ?
Pkg-Description: ?
Remark: ESRF can you gives more information about this software

Suggests: dyndom3d
Homepage: http://fizz.cmp.uea.ac.uk/dyndom/3D/
License: non-free
Pkg-Description: DynDom3D is a new program for the analysis of domain
 movements in large, multi-chain, biomolecular complexes. The program
 is applicable to any molecule for which two atomic structures are
 available that represent a conformational change indicating a
 possible domain movement. Unlike the original DynDom (DynDom1D) the
 method is blind to atomic bonding and atom type and can therefore be
 applied to biomolecular complexes containing different constituent
 molecules such as protein, RNA or DNA. At the heart of the method is
 the use of blocks located at grid points spanning the whole
 molecule. The rotation vector for the rotation of atoms from each
 block between the two conformations is calculated. Treating
 components of these vectors as coordinates means that each block is
 associated with a point in a “rotation space” and that blocks with
 atoms that rotate together, perhaps as part of the same rigid domain,
 will have co-located points. Thus a domain can be identified from the
 clustering of points from blocks within it. Domain pairs are accepted
 for analysis of their relative movements in terms of screw axes based
 upon a set of reasonable criteria. The results provide a depiction of
 the conformational change within each molecule that is easily
 understood, giving a perspective that is expected to lead to new
 insights. It has basically five parameters: a minimum domain size (in
 number of atoms), a ratio of interdomain displacement to intradomain
 displacement, a grid length, a block factor, and a block occupancy
 percentage.

Suggests: edna
Homepage: http://wiki.edna-site.org/index.php/Main_Page
License: ?
Pkg-Description: EDNA is a framework for developing plugin-based
 applications especially for online data analysis in the X-ray
 experiments field. This article describes the features provided by
 the EDNA framework to ease the development of extensible scientific
 applications. This framework includes a plugins class hierarchy,
 configuration and application facilities, a mechanism to generate
 data classes and a testing framework. These utilities allow rapid
 development and integration in which robustness and quality play a
 fundamental role. A first prototype, designed for macromolecular
 crystallography experiments and tested at several synchrotrons, is
 presented.

Suggests: elves
Homepage: http://ucxray.berkeley.edu/~jamesh/elves/
License: non-free
Pkg-Description: ?

Suggests: epmr
Homepage: http://www.epmr.info/
License: GPL2
Pkg-Description: EPMR is a general-purpose molecular replacement
 program. Unlike most molecular replacement programs, it does not
 divide the problem into separate rotation and translation
 searches. Instead, it uses an evolutionary search algorithm to
 simultaneously optimize the orientation and position of a search
 model (1,2). The program operates as follows:
 .
   * An initial set of random solutions (random orientations and
     positions for the search model) is generated.
   * The correlation coefficient is alculated for each trial solution.
   * A fraction of the highest scoring solutions are retained and used
     to regenerate a complete set of new trial solutions. This is done
     by applying random alterations to the orientation angles and
     translations for each “surviving” solution.  The correlation
     coefficients for the new population are calculated, the
     population is again regenerated from the top scoring solutions,
     and this procedure is repeated for a specified number of cycles.
 .
 The algorithm provides broad, stochastic, initial sampling of the
 search space while gradually focusing in on the most promising
 regions. It allows for efficient searching of the six-dimensional (or
 higher) space. In general, it is several orders of magnitude faster
 than a brute-force, systematic, 6-D search. At the end of the
 evolutionary optimization, a local minimization is performed on the
 best solution. This is simply a rigid-body refinement of the search
 molecule.
 .
 The program calculates structure factors rapidly by indexing into a
 molecular transform using the method of Huber and Schneider (3). A
 traditional structure factor calculation is done only once - for the
 search model set at the origin of a P1 cell. Subsequent structure
 factor calculations are done by transforming reflection indices
 according to the rotations and translations applied to the model and
 the relationship between the P1 and real cells, interpolating into
 the grid of P1 structure factors and summing over the symmetry
 operators of the crystal. This is much faster than an FFT
 calculation.  A simple Babinet-type solvent correction is applied to
 the calculated structure factors. The values of the solvent
 correction parameters (k, B) are optimized during the search.
 .
 Because of the stochastic nature of the evolutionary optimization
 process, the correct solution will not be obtained on every run, even
 with a very good search model. The success rate is dependent on the
 quality of the model (2). By default, 20 optimization attempts are
 done, and more may be required if you have a difficult problem. For
 search models that are poor and at the limit of detection, the search
 efficiency can be quite low. If you have a molecular replacement
 problem that has not yielded a solution by any other means, a
 reasonable last resort is to set up EPMR to do as many runs as your
 patience and computing resources will allow. As long as the true
 solution represents the global maximum in the correlation coefficient
 between Fo and Fc, even if by the slimmest of margins, the algorithm
 will eventually find it.
 .
 EPMR includes the following features:
   * the ability to automatically search for multiple copies of a
     molecule in the asymmetric unit, either sequentially or
     concurrently
   * the ability to search with multiple models, either sequentially
     or simultaneously (i.e., in competition with each other)
   * the ability to use multiple coordinate sets as parts of an
     “assembly” that comprises the complete search model
   * an option to search over all related space groups, either
     sequentially or simultaneously
   * rotation-only and translation-only search modes
   * an option to provide static, partial structure
   * independent optimization of each segment of a search model during
     the final rigid-body refinement step
   * an option to bypass the evolutionary search and do only local,
     rigid-body optimization of the model
Published-Authors: Charles R. Kissinger, Daniel K. Gehlhaar & David B. Fogel
Published-Title: “Rapid automated molecular replacement by evolutionary search”
Published-In: Acta Crystallographica, D55, 484-491 (1999).
Comment: contact the upstream for packaging.

Suggests: escet
Homepage: http://www.ifom-ieo-campus.it/escet/
License: non-free
Pkg-Description: ?
Remark: ESRF, still used ?, the homepage is dead

Suggests: evrouter
Homepage: http://www.bedroomlan.org/projects/evrouter
License: GPL
Pkg-Description: ?
Pkg-URL: http://debian.bedroomlan.org/debian/pool/main/e/evrouter/
Remark: ESRF, still used ?

Suggests: fit2d
Homepage: http://www.esrf.eu/computing/scientific/FIT2D/
License: non-free
Pkg-Description: ?
Comment: ?

Suggests: fobscom
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?

Recommends: gnuplot

Suggests: gramm
Homepage: http://vakser.bioinformatics.ku.edu/main/resources_gramm.php
License: ?
Pkg-Description: ?
Comment: ?

Suggests: grasp
Homepage: http://www.doe-mbi.ucla.edu/Software/GRASP.html
License: ?
Pkg-Description: ?
Comment: ?

Suggests: harker
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?

Suggests: hbplus
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?

Suggests: hca
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?

Suggests: hkl2map
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?

Suggests: hyss
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?

Recommends: imagej

Suggests: imosflm
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?

Suggests: induced-rad-dam
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?

Suggests: ipymol
Homepage: http://www.sbgrid.org/news/newsletters/2007/11
License: ?
Pkg-Description: ?
Comment: ?

Suggests: ispyb-client
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?

Recommends: jmol

Suggests: labelit
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?

Suggests: lam
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?

Suggests: laue
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?

Suggests: liged
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?

Suggests: ligplot
Homepage: ?
License: ?
Pkg-Description: ?
Comment: ?

Suggests: ligplus
Homepage: ?
License: ?
Pkg-Description: ?
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Suggests: molscriptmolscript-2.1.2
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Recommends: libmmdb2-0

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Recommends: pymol

Recommends: python

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Recommends: rasmol

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Suggests: shelx
Homepage: http://shelx.uni-ac.gwdg.de/SHELX/
License: free for academic
Pkg-Description: ?SHELX is a set of programs for crystal structure
 determination from single-crystal diffraction data. The first version
 of SHELX was written at the end of the 1960's. The gradual emergence
 of a relatively portable FORTRAN subset enabled it to be distributed
 (in compressed form including test data as one box of punched cards)
 in 1976. SHELX-76 survived unchanged - the extremely compact globally
 optimized code proved resistant to mutations - until major advances
 in direct methods theory made an update of the structure solution
 part necessary (SHELXS-86). Rewriting and validating the
 least-squares refinement part proved more difficult, but was finally
 achieved with the release of SHELXL-93. During this time operating
 systems such as RDOS, VMS and MSDOS, under which FORTRAN and SHELX
 flourished, rose and fell. Even punched cards became obsolete (except
 in Florida). The current version SHELX-97 is essentially upwards
 compatible with SHELX-76, for example the format of the reflection
 file remained unchanged (Microsoft please note). These programs are
 used in well over 50% of small-molecule structure
 determinations. Although SHELX was originally intended only for small
 molecules, improvements in computing performance and data collection
 methods have led to increased use of SHELX for macromolecules,
 especially the location of heavy atoms from MAD, SIR and SAD data
 using SHELXS (and recently SHELXD and SHELXE), and the refinement of
 proteins against high-resolution data (2.5A or better) using SHELXL.
 .
 SHELX-97 consists of the following programs:
 .
  * SHELXS - Structure solution by Patterson and direct methods
  * SHELXC - Preparations of files for macromolecular phasing with SHELXD and SHELXE
  * SHELXD - Structure solution for difficult problems (and location of heavy atom sites)
  * SHELXE - Phases from SHELXD heavy atom sites (and density modification)
  * SHELXL - Structure refinement (the version SHELXH is for large structures)
  * CIFTAB - Tables for publication via (small molecule) CIF format
  * SHELXA - Post-absorption corrections (for emergency use only)
  * SHELXPRO - Protein interface to SHELX
  * SHELXWAT - Automatic water divining for macromolecules
 .
 The program SHELXA was kindly donated by an anonymous user. It
 applies "absorption corrections" by fitting the observed to the
 calculated intensities as in the program DIFABS. SHELXA is intended
 for EMERGENCY USE ONLY, eg. when the world's only crystal falls off
 before there is time to make proper absorption corrections. Under no
 circumstances should the results be published; the anonymous author
 does not wish to be cited in this non-existent publication because it
 might ruin his reputation!

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Suggests: xdsme
Homepage: http://code.google.com/p/xdsme/
License: BSD
Pkg-Description: XDS Made Easier
 xdsme is a collection of python scripts made to simplify the
 processing of crystal diffraction images with the Wolfgang Kabsch's
 XDS Program (X-ray Detector Software,
 http://xds.mpimf-heidelberg.mpg.de/). Provided that the diffraction
 parameters are well recorded in the diffraction image headers, XDS
 data processing can be started with a simple command line like:

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Suggests: dials
Homepage: http://cci.lbl.gov/dials2/
License: BSD-3-clauses
Vcs-Browser: https://salsa.debian.org/science-team/dials
Vcs-Git: https://salsa.debian.org/science-team/dials.git
Pkg-Description: Diffraction Integration for Advance Light Source
 The field of structural biology by X-ray crystallography has
 benefitted greatly from technological advances in recent
 years. Automation, highly brilliant beamlines at 3rd generation
 synchrotron sources and high frame-rate pixel array detectors have
 together enabled extremely rapid collection of most MX datasets. In
 tandem, large area photon-counting detection, microfocus beams and
 high quality X-ray optics have brought more challenging projects
 within reach. At the cutting edge of this technological advance, the
 demonstration of FEL nano-crystallography offers the tantalizing
 prospect of a new era of structural biology at large facilities, with
 a concomitant step change in data rates and requirements for
 computationally intensive processing.
 .
 There is a clear need for new software for diffraction data analysis,
 designed to cope with the ever increasing volumes and rates of data
 collection, and with the developments in experimental methodology,
 from shutterless, fine-sliced rotation scans through to the
 randomly-oriented snapshots of serial crystallography. To keep up
 with these technological advances it is to be expected that this new
 software would utilize techniques of parallel processing using
 multiple CPU and GPU machines, facilitating not just speed, but
 highly accurate analysis based on a comprehensive physical model.

Suggests: gemmi
Homepage: https://github.com/project-gemmi/gemmi
License: MPL2 or LGPL3
Pkg-Description:
 Gemmi is a library, accompanied by a set of programs, developed
 primarily for use in macromolecular crystallography (MX). For working
 with:
    - macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files),
    - refinement restraints (CIF files),
    - reflection data (MTZ and mmCIF formats),
    - data on a 3D grid (electron density maps, masks, MRC/CCP4 format)
    - crystallographic symmetry.
 .
 Parts of this library can be useful in structural bioinformatics (for
 symmetry-aware analysis of protein models), and in other
 molecular-structure sciences that use CIF files (we have the fastest
 open-source CIF parser).
 .
 Gemmi is open-source (MPL) and portable – it runs on Linux, Windows,
 MacOS and even inside a web browser if compiled to WebAssembly. It is
 written in C++11, with Python (2 and 3) bindings, and with partial C
 and Fortran 2003 interface.
 .
 Occasionally, the project gets sidetracked into visualization of the
 PDB data.
 .
 Gemmi is a joint project of Global Phasing Ltd and CCP4.
 .
 The project is named after Gemmi Pass. The name can also be expanded
 as GEneral MacroMolecular I/o.