[Biojava-l] PDBFileParser and identifying atoms in ligands

[Andreas Prlic]

Hi Andy,

I see what you intend to do.  If you want just the HETATOM groups, you
can request them with

Chain.getAtomGroups(GroupType.HETATM);

or just amino acids groups you can requrest them  with

Chain.getAtomGroups(GroupType.AMINOACID);

same would work for getSeqresGroups(...) as well, but then your two
examples are quite specific:

193D is an antibiotic/DNA complex.
7EST chain I is a
TRIFLUOROACETYL-*L-*LEUCYL-*L-*ALANYL-P-TRIFLUOROMETHYLPHENYLANILIDE

Hetatoms are represented as Xs during the sequence alignments. I can
easily fix the "failing" alignment in this case, by ignoring the
wrongly aligned Hetatom Xs  (patch just committed to SVN...). Not sure
if it makes any biological difference in your two examples.

Andreas




On Fri, May 7, 2010 at 10:55 AM, Andy Thomas-Cramer
<thomascramera at dnastar.com> wrote:
>
> Hetatom groups are also used to represent modified residues in chains. I would like to obtain either the ligand atoms/groups without the sequence, or the sequence atoms/groups without the ligands.
>
> Chain.getSeqResGroups() reliably returns an empty list, when alignment fails and for non-amino sequences.
>
> Examples of the former include 193D (chains C) and 7EST (chain I). Both of these contain HETATMs both as modified residues and as ligands. Alignment fails in both.
>
> Interestingly, 193D's chain D is identical to chain C -- but it's alignment succeeds. One difference is that C has an associated ligand and D does not. Are the ligand atom groups associated with a chain considered during alignment?
>
>
> -----Original Message-----
> From: andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] On Behalf Of Andreas Prlic
> Sent: Thursday, May 06, 2010 3:52 PM
> To: Andy Thomas-Cramer
> Cc: biojava-l at lists.open-bio.org
> Subject: Re: [Biojava-l] PDBFileParser and identifying atoms in ligands
>
> Hi Andy,
>
> You don't need to process TERs to build up the representation of a
> structure.  The BioJava data model will work fine even if the file
> does not contain any amino acids. (e.g.  check 2KQO )
>
> Ligands will get represented as Hetatom groups in the datamodel.
> Check the Hetatom or Group javadocs for how to access their atoms.
>
> For your last question: Check out the Chain.getAtomGroups() and
> Chain.getSeqResGroups() methods...
>
> If it does not work the way you expect for a particular PDB ID, please
> let me know the ID, so I can take a look at the details.
>
> Andreas
>
>
> On Thu, May 6, 2010 at 9:50 AM, Andy Thomas-Cramer
> <thomascramera at dnastar.com> wrote:
>> >From a PDB file, I can identify which atoms are in ligands, and which
>> are in residues in the chain. The chain atoms end with the TER record.
>>
>>
>>
>> >From the BioJava API, I can distinguish as well -- if it's an amino
>> sequence and the automatic alignment between SEQRES and ATOM sequences
>> is successful.
>>
>>
>>
>> Is there a way through the API to identify atoms in ligands, when the
>> chain is not an amino sequence or alignment fails? It looks like the TER
>> record is ignored by PDBFileParser.
>>
>>
>>
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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