Pete,
I don't think so. The pdbset output does not match the SEQRES
definition in PDB format version 2.3 and I didn't find any changes in
the upstream versions. Plus, the pdbset output does not match the
SEQRES record in the pdb-file downloaded from PDB, and it's unlikely
that format was changed without applying those changes to files in the
database.
It seems to me that posting in ccp4bb is one of the correct ways to
report a problem. Am I wrong? The other option is to send it to
[log in to unmask], but I assume that this address is subscribed to ccp4bb
anyway.
Ed.
On Thu, 2008-07-10 at 14:42 -0700, Dunten, Pete W. wrote:
> 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
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
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