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
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
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