[BiO BB] SEQRES and ATOM record mismatch

James Stroud jstroud at mbi.ucla.edu
Wed Dec 8 17:42:08 EST 2004

Will a tool that pulls sequence from the ATOM records help?

If so, I have written one that does this. It can do it programatically (ie 
automatically for a large number of sequences). I can send it to you if you 
like. It is part a python API. I am still developing it, so there is no 
documentation, but I can write the two or three lines of code required to use 
it for this purpose.


On Wednesday 08 December 2004 01:10 pm, Goel, Manisha wrote:
> Dear All,
> I have been using protein sequences of proteins with known structures
> (PDB databse) derived from the SEQRES records.
> But now that I need to run either DSSP or STRIDE on them.. I cannot map
> the secondary structure back to the sequence alignments because the
> SEQRES and ATOMS records do not agree on the residue number id.
> So a residue numbered as 278 in SEQRES record is listed as 268 in the
> ATOMS record, messing up my alignments (I was using this numbering to
> map the secondary structure on to the sequence)
> I have come across quite a bit of discussion in some mailing lists about
> the need & proposed methods of modification of the PDB files, so that
> they can be made consistent.
> BUT ..
> Meanwhile can somebody suggest a method or resource .. which could
> either fix this dicrepency or maybe a round about way of taking care of
> this.
> I guess with people working with stuctural/sequence mapping so often,
> some such fix would have definetly been devised by somebody.
> I just want to be able to modify the residue numbers in the ATOMS record
> to match the SEQRES records or something to that effect. CIF does not
> work because it does not segregate by chain numbers/id.
> Thanks for any input,
> -MAnisha

James Stroud, Ph.D.
UCLA-DOE Institute for Genomics and Proteomics
611 Charles E. Young Dr. S.
MBI 205, UCLA 951570
Los Angeles CA 90095-1570

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