Shows how to locally refine a fit of a protein inside its density using a MC/CG optimization protocol. This example does not necessarily converges to the global minimum as that may require more optimization steps. If one wishes to use this example as a template for real refinement purposes, please adjust the parameters of the function IMP.em.local_rigid_fitting accordingly.
37 dmap.get_header_writable().set_resolution(resolution)
46 sampled_input_density.set_particles(ps)
47 sampled_input_density.resample()
48 sampled_input_density.calcRMS()
52 dmap, sampled_input_density, sampled_input_density.get_header().dmin)
53 print "The CC score of the native transformation is:", best_score
60 IMP.algebra.get_unit_bounding_box_3d())
62 rand_angle = random.uniform(-70. / 180 * math.pi, 70. / 180 * math.pi)
78 sampled_input_density.resample()
79 sampled_input_density.calcRMS()
82 dmap, sampled_input_density, sampled_input_density.get_header().dmin)
84 print "The start score is:", start_score,
"with rmsd of:", start_rmsd
87 print "preforming local refinement, may run for 3-4 minutes"
92 sampled_input_density.resample()
93 sampled_input_density.calcRMS()
96 dmap, sampled_input_density, sampled_input_density.get_header().dmin)
97 print "The score after centering is:", score2,
"with rmsd of:", rmsd
105 mh.get_particle(), refiner,
111 print "The start score is:", start_score,
"with rmsd of:", start_rmsd
112 for i
in range(fitting_sols.get_number_of_solutions()):
120 print "Fit with index:", i,
" with cc: ", 1. - fitting_sols.get_score(i),
" and rmsd to native of:", rmsd
123 prot_rb, fitting_sols.get_transformation(i).get_inverse())