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|
Bead model alignment
....................
Here are presented some basics way to use beed-model alignment in FreeSAS as a library.
Some abbreviations:
- DA = Dummy Atom
- DAM = Dummy Atoms Model
- NSD = Normalized Spatial Discrepancy
The SASModel class
""""""""""""""""""
This class allows to manipulate a DAM and to do some operations on it as
it is presented here.
First, the method SASModel.read() can be used to read a pdb file
containing data of a DAM :
.. code-block:: python
from freesas.model import SASModel
model1 = SASModel() #create SASModel class object
model1.read("dammif-01.pdb") #read the pdb file
#these 2 lines can be replaced by model1 = SASModel("dammif-01.pdb")
print(model1.header) #print pdb file content
print(model1.atoms) #print dummy atoms coordinates
print(model1.rfactor) #print R-factor of the DAM
Some informations are extracted of the model atoms coordinates:
- fineness : average distance between a DA and its first neighbours
- radius of gyration
- Dmax : DAM diameter, maximal distance between 2 DA of the DAM
- center of mass
- inertia tensor
- canonical parameters : 3 parameters of translation and 3 euler
angles, define the transformation to applied to the DAM to put it
on its canonical position (center of mass at the origin, inertia axis
aligned with coordinates axis)
.. code-block:: python
print(model1.fineness) #print the DAM fineness
print(model1.Rg) #print the DAM radius of gyration
print(model1.Dmax) #print the DAM diameter
model1.centroid() #calculate the DAM center of mass
print(model1.com)
model1.inertiatensor() #calculate the DAM inertiatensor
print(model1.inertensor)
model1.canonical_parameters() #calculate the DAM canonical_parameters
print(model1.can_param)
Other methods of the class for transformations and NSD calculation:
.. code-block:: python
param1 = model1.can_param #parameters for the transformation
symmetry = [1,1,1] #symmetry for the transformation
model1.transform(param1, symmetry)
#return DAM coordinates after the transformation
model2 = SASModel("dammif-02.pdb") #create a second SASModel
model2.canonical_parameters()
atoms1 = model1.atoms
atoms2 = model2.atoms
model1.dist(model2, atoms1, atoms2)#calculate the NSD between models
param2 = model2.can_param
symmetry = [1,1,1]
model1.dist_after_movement(param2, model2, symmetry)
#calculate the NSD, first model on its canonical position, second
#model after a transformation with param2 and symmetry
The AlignModels class
"""""""""""""""""""""
This other class contains lot of tools to align several DAMs, using the
SASModel class presented before.
The first thing to do is to select the pdb files you are interested in
and to create SASModels corresponding using the method of the class like
following :
.. code-block:: python
from freesas.align import AlignModels
inputfiles = ["dammif-01.pdb", "dammif-02.pdb", "dammif-03.pdb", ...]
align = AlignModels(inputfiles) #create the class
align.assign_models() #create the SASModels
print(align.models) #SASModels ready to be aligned
Next, the different NSD between each computed models can be calculated
and save as a 2d-array. But first it is necessary to give which models are
valid and which ones are not and need to be discarded :
.. code-block:: python
align.validmodels = numpy.ones((len(align.inputfiles)))
#here we keep all models as valid ones
align.makeNSDarray() #create the NSD table
align.plotNSDarray() #display the table as png file
align.find_reference() #select the reference model
align.alignment_reference() #align models with the reference
SuPyComb script
...............
| FreeSAS can also be used directly using command lines. Here is
presented the way to use the program supycomb, the re-implementation
of the supcomb of the
`Atsas package <http://dx.doi.org/10.1107/S0021889800014126>`_.
| Supycomb has two different process, the first one is called when only
two pdb files are put as arguments and a second one for more than two
files.
| With the first process, the program creates the two DAM provided by pdb
files and align the second one on the first one (reference, do not move).
The coordinates of the atoms of the aligned model are saved in a pdb file
and the program return the final NSD between the two DAM. The name of the
output can be modified.
| The second one creates a model for each file put as argument. Models are
first selected as valid or not using its R-factor value. The maximum
value is the mean of R-factors plus twice the standard deviation. The
figure of the R-factors is then displayed or saved automatically in png
format.
| Next, NSD between each valid DAM are computed to select best models
using the mean of NSD with other models for each DAM. A maximal value
for the NSD mean is create as the mean of the ND mean plus a standard
deviation to discarded the to different models. The model with the lower
NSD mean is the reference one. A second figure with the NSD table and the
graphic with the NSD means is displayed or saved.
| Finally, the valid models are aligned on the reference one and final
positions are saved in pdb files called model-01.pdb, model-02.pdb, etc...
| Several options are available for the supycomb program:
.. command-output:: supycomb --help
| Slow mode / fast mode:
| For the slow mode, the optimization of the NSD is done for each symmetry
(ie. 8 times) whereas for the fast mode, the best symmetry is first
chosen without optimization and only the NSD for this symmetry is
optimized.
The result is that the slow mode is nearly 8 times slower than the fast
one. The NSD values thought are a few lower using the slow mode.
| Enantiomorphs option:
| This option can be used to authorize or not the program to look for
enantiomorphs. If not, the program will not test 8 symmetries but only 4.
The execution time will be nearly twice lower without enantiomorphs but
only if you are using the slow mode, the gain is negligible for the fast
mode. Moreover, it will not be able to recognize two enantiomorphs of the
same protein.
| GUI option:
| If you choose to display the computed figures during the execution of
the program to save it or not, so to use the Graphical User Interface,
you have to select this option as "YES" (set by default). It is also
possible to save it automatically as png files by setting the option as
"NO".
| Output option:
| This option allow to change the default filename of the output for the
two models alignment process. It has to be a .pdb file !
|
