IMP  2.3.1
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 import IMP
6 import IMP.atom
7 import IMP.em
8 m = IMP.kernel.Model()
9 # 1. read a protein and get its bounding box dimension
10 sel = IMP.atom.CAlphaPDBSelector()
11 # read protein
12 mh = IMP.atom.read_pdb(IMP.em.get_example_path("input.pdb"), m, sel)
13 apix = 1.
14 resolution = 6.
15 # compute bbox, and map size in voxels
16 bbox = IMP.atom.get_bounding_box(mh)
17 #diag = bbox.get_corner(0) - bbox.get_corner(1)
18 #nx = int(bboxCoverage * diag[0] / apix)
19 #ny = int(bboxCoverage * diag[1] / apix)
20 #nz = int(bboxCoverage * diag[2] / apix)
21 
22 # create a density header of the requested size
23 dheader = IMP.em.create_density_header(bbox, apix)
24 dheader.set_resolution(resolution)
25 dmap = IMP.em.SampledDensityMap(dheader)
26 ps = IMP.core.get_leaves(mh)
27 dmap.set_particles(ps)
28 # dmap.get_header_writable().set_number_of_voxels(nx,ny,nz)
29 dmap.resample()
30 dmap.calcRMS()
31  # computes statistic stuff about the map and insert it in the
32  # header
33 print dmap.get_header().show(), "\n"
34 IMP.em.write_map(dmap, "map.mrc", IMP.em.MRCReaderWriter())