IMP  2.3.1
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
10 # read protein
12 mh = IMP.atom.read_pdb(IMP.em.get_example_path("input.pdb"), m, sel)
13 # add radius info to each atom, otherwise the resampling would fail.
15 ps = IMP.core.get_leaves(mh)
16 # decide on resolution and spacing you would like to simulate to
17 resolution = 10.
18 apix = 1.5
19 dmap = IMP.em.particles2density(ps, resolution, apix)
20 # write out the map in the favorite format (xplor, mrc, em and spider are
21 # supported)
22 IMP.em.write_map(dmap, "example.mrc", IMP.em.MRCReaderWriter())