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IMP Reference Guide  2.6.0
The Integrative Modeling Platform
em/generate_density_map_of_fixed_dimension.py

Shows how to generate a density map of fixed dimension and how to sample particles within this density map.

1 ## \example em/generate_density_map_of_fixed_dimension.py
2 # Shows how to generate a density map of fixed dimension and how to sample
3 # particles within this density map.
4 
5 from __future__ import print_function
6 import IMP
7 import IMP.atom
8 import IMP.em
9 import sys
10 
11 IMP.setup_from_argv(sys.argv, "generate a density map of fixed dimension")
12 
13 m = IMP.Model()
14 # 1. read a protein and get its bounding box dimension
15 sel = IMP.atom.CAlphaPDBSelector()
16 # read protein
17 mh = IMP.atom.read_pdb(IMP.em.get_example_path("input.pdb"), m, sel)
18 apix = 1.
19 resolution = 6.
20 # compute bbox, and map size in voxels
21 bbox = IMP.atom.get_bounding_box(mh)
22 #diag = bbox.get_corner(0) - bbox.get_corner(1)
23 #nx = int(bboxCoverage * diag[0] / apix)
24 #ny = int(bboxCoverage * diag[1] / apix)
25 #nz = int(bboxCoverage * diag[2] / apix)
26 
27 # create a density header of the requested size
28 dheader = IMP.em.create_density_header(bbox, apix)
29 dheader.set_resolution(resolution)
30 dmap = IMP.em.SampledDensityMap(dheader)
31 ps = IMP.core.get_leaves(mh)
32 dmap.set_particles(ps)
33 # dmap.get_header_writable().set_number_of_voxels(nx,ny,nz)
34 dmap.resample()
35 dmap.calcRMS()
36  # computes statistic stuff about the map and insert it in the
37  # header
38 print(dmap.get_header().show(), "\n")
39 IMP.em.write_map(dmap, "map.mrc", IMP.em.MRCReaderWriter())