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IMP Reference Guide  develop.731656d855,2020/02/16
The Integrative Modeling Platform
em/pdb2density.py

A simple example showing how to simulate density from a protein. IMP uses a Gaussian smoothing kernel. see SampledDensityMap::resample for documentation.

1 ## \example em/pdb2density.py
2 # A simple example showing how to simulate density from a protein.
3 # IMP uses a Gaussian smoothing kernel. see SampledDensityMap::resample for documentation.
4 #
5 
6 import IMP.em
7 import IMP.core
8 import IMP.atom
9 import sys
10 
11 IMP.setup_from_argv(sys.argv, "pdb2density")
12 
13 m = IMP.Model()
14 # read protein
16 mh = IMP.atom.read_pdb(IMP.em.get_example_path("input.pdb"), m, sel)
17 # add radius info to each atom, otherwise the resampling would fail.
19 ps = IMP.core.get_leaves(mh)
20 # decide on resolution and spacing you would like to simulate to
21 resolution = 10.
22 apix = 1.5
23 dmap = IMP.em.particles2density(ps, resolution, apix)
24 # write out the map in the favorite format (xplor, mrc, em and spider are
25 # supported)
26 IMP.em.write_map(dmap, "example.mrc", IMP.em.MRCReaderWriter())