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

vanitha@cs.wisc.edu vanitha at cs.wisc.edu
Thu Mar 16 15:46:24 CET 2006


Thanks a lot for your responses. How do I access these proteins once I add
them to the universe? Is there a "for protein in Universe.Protein" kind of
iterator?

Thanks,

- Vanitha


> 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.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Laboratoire Léon Brillouin, CEA Saclay,
> 91191 Gif-sur-Yvette Cedex, France
> Tel.: +33-1 69 08 79 25
> Fax: +33-1 69 08 82 61
> E-Mail: konrad.hinsen at cea.fr
> ---------------------------------------------------------------------
>
>
>
>





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