[MMTK] Correct Hydrogens

Konrad Hinsen hinsen at cnrs-orleans.fr
Thu May 27 16:40:12 CEST 2004


On May 26, 2004, at 23:35, Stuart Murdock wrote:

> 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.

Do I understand correctly that by "editing files" you mean editing 
PDB.py to remove the hydrogen code? In that case, the cleanest solution 
is to write your own code for dealing with the items in a PDB file, 
which is probably just a few lines since you don't need to deal with 
lots of special cases. An example:

conf = PDB.PDBConfiguration('protein.pdb')
chains = []
for chain in conf.peptide_chains:
     chains.append(Proteins.PeptideChain(chain))
protein = Proteins.Protein(chains)

Actually, this probably does exactly what you want.

Konrad.
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