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

Bernd Web bernd.web at gmail.com
Fri Sep 15 19:09:22 EDT 2006


Hi,

Regarding the pdb parsing. Jurgen writes:

# my $struc = $stream->next_structure();
# my $chain = $struc->next_chain();
# my $res = $chain->next_residue();
but the implementation ran into severe reference management trouble.

I am not into StructureIO, but given this I would not feel like
rewriting to this structure again, since apparently it was originally
like this.

Regarding the HETATMs after TER in the PDB records that are included
in the residue chains: looking through the code it is due to a "bug"
that was solved:  fix for bug #1187 for 1abm.
Before this bugfix a chain A with residues and a chain A with HETATMS
was created. So rolling this back partly solves the point about
HETATMS.

In case there is only one chain, like Jurgen says, it is ambiguous to
state that HETATMs are non-chain, since the chain and the HETATMs
(mostly HOH) are all not labelled. However, here I would take the
chain only to TER.

Like Dave said: difference of interpretation ;-) I wrote about my
interpretation and will try to adapt pdb.pm accordingly....

Bernd


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