[Biojava-l] PDBFileParser and identifying atoms in ligands

[Andy Thomas-Cramer]

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.
>
>
>
>
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