IMP  2.1.1
The Integrative Modeling Platform
em/fit_restraint.py

A simple example showing how to set up a fit restraint. The number of spheres and resolution are randomly chosen and so should not be considered significant.

1 ## \example em/fit_restraint.py
2 # A simple example showing how to set up a fit restraint. The number of
3 # spheres and resolution are randomly chosen and so should not be
4 # considered significant.
5 
6 import IMP.em
7 import IMP.core
8 import IMP.atom
9 IMP.base.set_log_level(IMP.base.SILENT)
10 m = IMP.kernel.Model()
11 # 1. setup the input protein
12 # 1.1 select a selector.
14 # 1.2 read the protein
15 mh = IMP.atom.read_pdb(IMP.em.get_example_path("input.pdb"), m, sel)
16 ps = IMP.core.get_leaves(mh)
18 # 2. read the density map
19 resolution = 8.
20 voxel_size = 1.5
21 dmap = IMP.em.read_map(
23 dmap.get_header_writable().set_resolution(resolution)
24 # 3. calculate the cross correlation between the density and the map
25 print "The cross-correlation score is:", 1. - IMP.em.compute_fitting_score(ps, dmap)
26 # 4. add a fitting restraint
27 r = IMP.em.FitRestraint(ps, dmap)
28 m.add_restraint(r)
29 print "The fit of the particles in the density is:", r.evaluate(False)