[BiO BB] SEQRES and ATOM record mismatch

Goel, Manisha MAG at Stowers-Institute.org
Wed Dec 8 16:10:17 EST 2004

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
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,

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