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.

## \example 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.
#

import IMP.em
import IMP.core
import IMP.atom
import sys

IMP.setup_from_argv(sys.argv, "pdb2density")

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