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

Brian Osborne osborne1 at optonline.net
Thu Sep 14 11:16:50 EDT 2006


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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