[Bioperl-l] PDB sequence from ATOM records
Matthew.Betts at ii.uib.no
Wed Jul 7 05:05:26 EDT 2004
Thanks for all the replies. I definitely agree that we should sort out
what's wanted from Bio::Structure before changing what's already there. If
there's a session at BOSC (maybe in conjunction with 3Dsig?) could someone
post the conclusions somewhere so that those of us who can't make it can
comment? Thanks. Also, the MSD people must have done a lot of this type of
thing already, and their input would be really useful (f.eks probably
a good idea to use their API).
On Tue, 6 Jul 2004 bioperl-l-request at portal.open-bio.org wrote:
Date: Tue, 06 Jul 2004 15:54:38 +0100
From: Dave Howorth <dhoworth at mrc-lmb.cam.ac.uk>
Subject: Re: [Bioperl-l] PDB sequence from ATOM records
To: bioperl-l at portal.open-bio.org
Message-ID: <40EABD2E.5020602 at mrc-lmb.cam.ac.uk>
Content-Type: text/plain; charset=us-ascii; format=flowed
It seems to me that many people who parse PDB files write their own
code. This is a shame, because it wastes effort, it makes things more
difficult for beginners, and it leads to differences in results.
This practice stems, I believe, both from the complexity of the PDB data
and from the multitude of use cases. It is well-known that there are
exceptions to almost every rule about the content of PDB files. It is
also clear that sometimes people care about every character in the
coordinates, while other times they care just about the sequence and
sometimes just specific parts of the header, for example.
I think it might be useful to have a session on this subject at BOSC.
We can try to capture different people's requirements. We can list
examples of PDB entries that demonstrate specific problems. We can
consider existing code possibilities. We can drink beer.
Afterwards, perhaps there is more chance of building some software that
will be widely used.
What do you think?
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