[MMTK] Creating a Protein object from one chain of the PDB

Konrad Hinsen konrad.hinsen at cea.fr
Wed Mar 15 17:43:47 CET 2006


On Mar 14, 2006, at 14:37, vanitha at cs.wisc.edu wrote:

> Sorry for the spate of emails. I have a question that is probably  
> trivial
> for most of you. I have a PDB that has two chains A & B. How do I
> construct two Protein objects from these within MMTK? Sample code  
> will be
> greatly appreciated.

from MMTK import *
from MMTK.PDB import PDBConfiguration
from MMTK.Proteins import Protein

universe = InfiniteUniverse()

conf = PDBConfiguration('some_file.pdb')
chains = conf.createPeptideChains()
for chain in chains:
     universe.addObject(Protein(chain))


Note that creating separate protein objects for each chain will not  
detect disulfide bridges between the chains.

Konrad.
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Konrad Hinsen
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E-Mail: konrad.hinsen at cea.fr
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