IMP  2.0.1
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
9 m= IMP.Model()
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 supported)
21 IMP.em.write_map(dmap,"example.mrc",IMP.em.MRCReaderWriter())