[MMTK] Correct Hydrogens

Eric Zollars zollars at caltech.edu
Thu May 27 00:56:24 CEST 2004

    My first thought on this would be:

from MMTK import *
from MMTK.PDB import PDBConfiguration
conf = PDBConfiguration('blah.pdb')
chains = conf.createPeptideChains('no_hydrogens')

But I may be missing something?

Stuart Murdock wrote:

> Hi
> I have PDB formatted files (for proteins) which have some missing 
> hydrogen atoms. I would like
> to be able to read them into MMTK from the PDB file without the 
> correct additional hydrogens being
> introduced by MMTK. I would like to analyse sub-sections of proteins 
> with MMTK, which are not the
> complete molecule.
> I can currently do this by simply not performing the
> chain.findHydrogenPositions()
> statement in the file PDB.py when creating peptide chains and deleting 
> any undefined atoms, but was
> wondering if there was a cleaner way of doing this without editing any 
> files.
> Any suggestions would be great.
> Thanks,
> Stuart

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