simulate_density_from_pdb.py

#!/usr/bin/env python

import IMP.em

def main():
    IMP.base.set_log_level(IMP.base.SILENT)
    usage = """%prog [options] <complex.pdb>
           <output: density.mrc> <resolution> <a/pix>

Samples a protein into a simulated 3D density map."""
    parser = IMP.OptionParser(usage=usage, imp_module=IMP.em)
    (options, args) = parser.parse_args()
    if len(args) != 4:
        parser.error("incorrect number of arguments")
    pdb_fn=args[0]
    mrc_fn=args[1]
    resolution=float(args[2])
    apix=float(args[3])
    #read the protein
    mdl=IMP.Model()
    mh=IMP.atom.read_pdb(pdb_fn,mdl,IMP.atom.NonWaterNonHydrogenPDBSelector())
    IMP.atom.add_radii(mh)
    #sample the density
    dmap = IMP.em.particles2density(IMP.core.get_leaves(mh),resolution,apix)
    IMP.em.write_map(dmap,mrc_fn,IMP.em.MRCReaderWriter())

if __name__ == "__main__":
    main()