[Bioperl-l] PDB sequence from ATOM records

Matthew Betts Matthew.Betts at ii.uib.no
Thu Jul 1 10:50:46 EDT 2004


I need to be able to map some protein sequence alignment information on to 
a protein structure. To do this I need to get the sequence from the ATOM 
records, since the SEQRES sequence is often not exactly the same.

So I'd like to change Bio::Structure::Residue a little:

Amino-acid type and residue number are currently contained in one value, 
residue->id. I would like to separate them in to two, residue->type 
and residue->num. Then, for backwards compatibility, construct residue->id 
from these each time it is required (or store it as well if that is 
better?). residue->type should be able to return the one-letter code as 
well as the three-letter code.

And then have a method called something like Bio::Structure::Entry->atom_seq 
that would return a Bio::PrimarySeq object constructed from the one-letter 
codes of the residues of a particular chain.

Any comments please... Thanks.


P.S. Sorry if this message is a repeat - our email server went down as I 
was sending it the first time.

Matthew Betts, mailto:matthew.betts at ii.uib.no
Phone: (+47) 55 58 40 22, Fax: (+47) 55 58 42 95
CBU, BCCS, HiB, UNIFOB / Universitetet i Bergen
Thormøhlensgt. 55, N-5008 Bergen, Norway

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