[BiO BB] what the difference between remediated pdb and pdb?

[Roberto Mosca]

 From the document:

"3.5 Resolution macromolecular sequence conflicts
Differences in entity sequence assignment between RCSB PDB and MSD-EBI  
have
been resolved. Any remaining differences between the chemical sequence  
and the
macromolecular sequence have also been resolved."

I think that this refers only to the DBREF and SEQRES records in the  
file. Of
course an alanine cannot become a valine or a tyrosine when going from  
the original
to the remediated PDB.

I'm not sure what kind of errors have been fixed but I think there  
could have been
inconsistencies between the sequence reported in the SEQRES records  
and the
sequence corresponding to the ATOM records in the PDb file itself.

Roberto

............................................
  Dr. Roberto Mosca

  EMBL c/o DESY
  Notkestr. 85
  22607 Hamburg
  Germany

  Email: roberto.mosca at embl-hamburg.de
  Tel:   +49 (0)40 89902 131
  Web:   http://www.embl-hamburg.de/~rmosca
............................................



On Jun 8, 2008, at 04:03, Xue Li wrote:

> Hello all,
>
>> From remediated pdb web site http://remediation.wwpdb.org/ 
>> index.html, I read
> "Updated references to databases and taxonomies and Resolved  
> differences
> between chemical and macromolecular sequences".
>
> Does it mean that for some proteins they will have  difference  
> sequences in
> remediated pdb and ordinary pdb?
>
> Thanks.
>
> -- 
> Xue, Li
> Bioinformatics and Computational Biology program @ ISU
> Ames, IA 50010
> 515-450-7183
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>