[Bioperl-l] More on PDB and chains...

Bernd Web bernd.web at gmail.com
Thu Sep 14 11:56:09 EDT 2006


Hi,

HETATM sometimes are present in a chain. So we cannot just exclude all
HETATMS from a chain. However, since a chain is terminated with TER we
could indeed store all non-chain HETATMs in an object (indeed like
$struc->get_hetatm).

What would be nice is to be able to see if a "residue" IN a chain is a
HETATM. (Sometimes) modified residues (e.g. CME) are also labelled
HETATM. At least internally to Structure::pdb it is clear what are
HETATMs since the PDB files are written (almost) correctly.
I used a script on
http://lists.open-bio.org/pipermail/bioperl-guts-l/2005-November/020116.html
to write PDB from 8HVP. In this case indeed at each "border" between
ATOM and HETATOM within the chain a TER is printed where the original
record has ATOM. Look for ABA and LOV HETATMS in the chain.

Indeed I agree that non-chain HETATMs should not be part of the default chain.
So a PDB record (e.g. 102L) with only one chain should have the
protein chain and a separate HETATM "chain".

Bernd

On 9/14/06, Brian Osborne <osborne1 at optonline.net> wrote:
> Bernd,
>
> I¹m taking this discussion back into bioperl-l. You've uncovered a slightly
> different bug then. Shouldn't the HETATMs always be in a separate "chain"
> regardless of whether there are 1 or more than 1 polypeptide chains? So
> that¹s one question.
>
> Related question: shouldn't the get_chains() method only return polypeptide
> chains, just as they're described in the PDB file? I would think that you'd
> retrieve the HETATMs using something like:
>
> my $hetatm = $struc->get_hetatm
>
> In the PDB file if there are, say, 3 chains the get_chains() method returns
> 4. One of these is the HETATMs ³chain² labelled by the id Œdefault¹. I don¹t
> think this is right since, first, the heteroatoms do no constitute a ³chain²
> and, second, the PDB file itself states that there are 3 chains. Perhaps
> users of StructIO::pdb have other points of view?
>
> Brian O.
>
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