[MMTK] Missing residue on chain due to altloc field

khinsen@cea.fr khinsen at cea.fr
Tue Jan 24 13:07:54 CET 2006

On Jan 23, 2006, at 19:50, Peter wrote:

> Yes, another PDB problem to report ;)

Are you working through the whole PDB?

> Is the problem here that by using a default of "A", neither altloc "1"
> or "2" is used - resulting in the residue being ignored?

Yes, exactly.

> Looking though the help, Scientific.IO.PDB.Structure takes an optional
> argument alternate_code defaulting to "A", but I don't see how to
> specify this at the MMTK level.

I have just added the same two optional arguments to  
MMTK.PDB.PDBConfiguration(). With the existing releases, you have to  
use a workaround:

	class MyPDBConfiguration(MMTK.PDB.PDBConfiguration):

		def __init__(self, filename, alternate_code):
			MMTK.PDB.PDBConfiguration.__init__(self, filename)
			self.my_alternate_code = alternate_code

		def parseFile(self, file):
			self.alternate = self.my_alternate_code
			MMTK.PDB.PDBConfiguration.parseFile(self, file)

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: khinsen at cea.fr

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