mdtraj selection

selection.py

import mdtraj as md
import simtk.openmm.app as app
import pdbfixer

fixer = pdbfixer.PDBFixer(pdbid='4fmu')
fixer.findMissingResidues()
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
fixer.findMissingAtoms()
fixer.addMissingAtoms()
#fixer.addMissingHydrogens(7.0)
app.PDBFile.writeFile(fixer.topology, fixer.positions, open("./4fmu_addmissing.pdb", 'w'))


t = md.load("4fmu_addmissing.pdb")

indices0 = t.top.select("water or (resname ZN)")
indices1 = t.top.select("protein and (resSeq 11 to 259)")
indices = np.concatenate((indices0, indices1))

t.atom_slice(indices, inplace=True)
t.save("./4fmu_truncated.pdb")


fixer = pdbfixer.PDBFixer(filename="4fmu_truncated.pdb")
fixer.findMissingResidues()
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
fixer.findMissingAtoms()
fixer.addMissingAtoms()
fixer.addMissingHydrogens(7.0)
app.PDBFile.writeFile(fixer.topology, fixer.positions, open("./4fmu_fixed.pdb", 'w'))