[phenixbb] pdb hierarchy

[Pavel Afonine]

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<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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