[Bioperl-l] PDB sequence from ATOM records

Matthew Betts 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:

Message: 10
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?

Cheers, Dave
Dave Howorth
MRC Centre for Protein Engineering
Hills Road, Cambridge, CB2 2QH
01223 252960

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