[phenixbb] pdb hierarchy

Jeff Headd jjheadd at lbl.gov
Sat Dec 3 14:46:10 PST 2011

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.


On Sat, Dec 3, 2011 at 1:26 PM, Bradley Hintze <bradley.hintze at duke.edu> 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
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