Re: [phenixbb] pdb hierarchy

This once again shows that having duplicate chain IDs in PDb file is a very bad idea. Pavel On 12/3/11 2:46 PM, Jeff Headd wrote:

Hi Bradley,

The PDB hierarchy separates ligands and waters from protein/RNA, so if you have waters or ligands that are part of chain 'A', they will end up in the hierarchy as separate chains, but also with chainID 'A'. Similarly, if you have a TER card in the middle of a chain, that will also be split into separate chains within the hierarchy.

Jeff

On Sat, Dec 3, 2011 at 1:26 PM, Bradley Hintze wrote:

...

Hi Phenix,

I have a hierarchy question.

I was using the hierarchy and got something that I did not expect. when running this:

pdb_io = pdb.input(pdbfile) hierarchy = pdb_io.construct_hierarchy()

for model in hierarchy.models(): print model.id for chain in model.chains(): print ' ' + chain.id

When I do this I expect the chains in pdbfile to be printed once for each model in pdbfile. However, when I ran this I got, for example, chain 'A' printed four times under the same model. Why is this?

Thanks, Bradley

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb