Is this just a consequence of old/new conventions for the SEQRES records?
If so, send a feature request to ccp4, asking for an option to be added to pdbset.
Pete
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Ed Pozharski
Sent: Thursday, July 10, 2008 2:31 PM
To: [log in to unmask]
Subject: [ccp4bb] pdbset bug - seqres record
There is a bug in pdbset: when you output a sequence (using "SEQU PDB"), the residue names are shifted to the left by one position. Here is how it looks like:
In PDB-file downloaded from the PDB:
SEQRES 5 A 171 ALA THR CYS ...
PDBSET output:
SEQRES 5 A 171 ALA THR CYS ...
I looked in the fortran code (CCP4 6.0.2) and it appears that this line:
6601 format ('SEQRES',i4,1x,a1,1x,i4,1x,13a4)
should be corrected like this
6601 format ('SEQRES',i4,1x,a1,1x,i4,2x,13a4)
I stumbled upon this when trying to insert SEQRES records into a pdb-file for processing in hydropro. Don't know if it's important anywhere else, but hydropro can't read the sequence if it's shifted.
--
Ed Pozharski <[log in to unmask]>
University of Maryland - Baltimore
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