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IMP Reference Guide  2.13.0
The Integrative Modeling Platform
saxs/profile.py

In this example, we read a protein from a PDB file and experimental profile file. Next we compute the theoretical profile from the PDB file and fit it to the experimental one.

This application is available as a web service at salilab.org/foxs. It is also available as C++ code in IMP/applications.

The experimental data for lysozyme is taken from crysol program (www.embl-hamburg.de/ExternalInfo/Research/Sax/crysol.html)

1 ## \example saxs/profile.py
2 # In this example, we read a protein from a PDB file and experimental profile file. Next we compute the theoretical profile from the PDB file and fit it to the experimental one.
3 #
4 # This application is available as a web service at salilab.org/foxs. It is also available as C++ code in IMP/applications.
5 #
6 # The experimental data for lysozyme is taken from crysol program (www.embl-hamburg.de/ExternalInfo/Research/Sax/crysol.html)
7 #
8 
9 from __future__ import print_function
10 import IMP
11 import IMP.atom
12 import IMP.core
13 import IMP.saxs
14 import os
15 import sys
16 
17 IMP.setup_from_argv(sys.argv, "profile")
18 
19 m = IMP.Model()
20 
21 #! read PDB
24 
25 #! read experimental profile
26 exp_profile = IMP.saxs.Profile(IMP.saxs.get_example_path('lyzexp.dat'))
27 
28 print('min_q = ' + str(exp_profile.get_min_q()))
29 print('max_q = ' + str(exp_profile.get_max_q()))
30 print('delta_q = ' + str(exp_profile.get_delta_q()))
31 
32 #! select particles from the model
33 particles = IMP.atom.get_by_type(mp, IMP.atom.ATOM_TYPE)
34 
35 #! calculate SAXS profile
36 model_profile = IMP.saxs.Profile()
37 model_profile.calculate_profile(particles)
38 model_profile.write_SAXS_file('6lyz.dat')
39 
40 #! calculate chi score (should be ~0.5 for this example)
41 saxs_score = IMP.saxs.ProfileFitterChi(exp_profile)
42 chi = saxs_score.compute_score(model_profile)
43 print('Chi = ' + str(chi))
44 
45 
46 #! convert to p(r)
48 model_profile.profile_2_distribution(pr, 48.0)
49 pr.normalize()
50 pr.show()