[BiO BB] SEQRES and ATOM record mismatch

Dr. Christoph Gille christoph.gille at charite.de
Wed Dec 8 16:58:57 EST 2004

I understand the problem as follows:
You have two sequences of the same protein, one derived from Calpha
positions and one from SEQRES. In loops where coordinate are not resolved
and no coordinates are recorded there will be a difference between both.

Align both with e.g.clustalW.

What scripting language are you using ?
In case you use java you are welcome to use the STRAP API.
It includes a very fast PDB-parser (30ms per PDB file) which also reads
SEQRES and also a dssp file parser.


> 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
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