IMP  2.4.0
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/applications.

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 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.
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 
16 
17 m = IMP.kernel.Model()
18 
19 #! read PDB
22 
23 #! read experimental profile
24 exp_profile = IMP.saxs.Profile(IMP.saxs.get_example_path('lyzexp.dat'))
25 
26 print('min_q = ' + str(exp_profile.get_min_q()))
27 print('max_q = ' + str(exp_profile.get_max_q()))
28 print('delta_q = ' + str(exp_profile.get_delta_q()))
29 
30 #! select particles from the model
31 particles = IMP.atom.get_by_type(mp, IMP.atom.ATOM_TYPE)
32 
33 #! add radius for water layer computation
35 for i in range(0, len(particles)):
36  radius = ft.get_radius(particles[i])
37  IMP.core.XYZR.setup_particle(particles[i], radius)
38 # compute surface accessibility
40 surface_area = s.get_solvent_accessibility(IMP.core.XYZRs(particles))
41 
42 #! calculate SAXS profile
43 delta_q = 0.5 / 500
44 model_profile = IMP.saxs.Profile(0.0, 0.5, delta_q)
45 model_profile.calculate_profile_partial(particles, surface_area)
46 # model_profile.write_SAXS_file('6lyz.dat')
47 
48 #! calculate chi score (should be ~0.5 for this example)
49 saxs_score = IMP.saxs.ProfileFitterChi(exp_profile)
50 chi = saxs_score.compute_score(model_profile)
51 print('Chi without parameter fitting = ' + str(chi))
52 
53 chi = (saxs_score.fit_profile(model_profile)).get_chi()
54 print('Chi after adjustment of excluded volume and water layer parameters = ' + str(chi))
55 saxs_score.fit_profile(model_profile, 0.95, 1.05, -2.0, 4.0, False,
56  '6lyz_fitted.dat')