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IMP Reference Guide  2.20.0
The Integrative Modeling Platform
saxs/profile_fit.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. Unlike in profile.py example, here we fit the profile with adjustment of the excluded volume and hydration layer density of the molecule.

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

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

1 ## \example saxs/profile_fit.py
2 # In this example, we read a protein from a PDB file and experimental profile
3 # file. Next we compute the theoretical profile from the PDB file and fit it
4 # to the experimental one. Unlike in profile.py example, here we fit the
5 # profile with adjustment of the excluded volume and hydration layer density
6 # of the molecule.
7 #
8 # This application is available as a web service at salilab.org/foxs. It is
9 # also available as C++ code in IMP at modules/foxs/bin/foxs.cpp.
10 #
11 # The experimental data for lysozyme is taken from crysol program
12 # (www.embl-hamburg.de/ExternalInfo/Research/Sax/crysol.html)
13 #
14 
15 from __future__ import print_function
16 import IMP
17 import IMP.atom
18 import IMP.core
19 import IMP.saxs
20 import sys
21 
22 IMP.setup_from_argv(sys.argv, "profile fit")
23 
24 m = IMP.Model()
25 
26 # read PDB
29 
30 # read experimental profile
31 exp_profile = IMP.saxs.Profile(IMP.saxs.get_example_path('lyzexp.dat'))
32 
33 print('min_q = ' + str(exp_profile.get_min_q()))
34 print('max_q = ' + str(exp_profile.get_max_q()))
35 print('delta_q = ' + str(exp_profile.get_delta_q()))
36 
37 # select particles from the model
38 particles = IMP.atom.get_by_type(mp, IMP.atom.ATOM_TYPE)
39 
40 # add radius for water layer computation
42 for i in range(0, len(particles)):
43  radius = ft.get_radius(particles[i])
44  IMP.core.XYZR.setup_particle(particles[i], radius)
45 # compute surface accessibility
47 surface_area = s.get_solvent_accessibility(IMP.core.XYZRs(particles))
48 
49 # calculate SAXS profile
50 delta_q = 0.5 / 500
51 model_profile = IMP.saxs.Profile(0.0, 0.5, delta_q)
52 model_profile.calculate_profile_partial(particles, surface_area)
53 # model_profile.write_SAXS_file('6lyz.dat')
54 
55 # calculate chi-square score (should be ~0.25 for this example)
56 saxs_score = IMP.saxs.ProfileFitterChi(exp_profile)
57 chi = saxs_score.compute_score(model_profile)
58 print('Chi without parameter fitting = ' + str(chi))
59 
60 chi = (saxs_score.fit_profile(model_profile)).get_chi_square()
61 print('Chi after adjustment of excluded volume and water layer parameters = '
62  + str(chi))
63 saxs_score.fit_profile(model_profile, 0.95, 1.05, -2.0, 4.0, False,
64  '6lyz_fitted.dat')