[Chimera-users] wwPDB Announcement: Release of Remediated PDB Data

Cathy Lawson cathy.lawson at rutgers.edu
Thu May 3 09:24:15 PDT 2007

***wwPDB Announcement: Release of Remediated PDB Data***

The wwPDB has collaborated on a project to remediate the PDB archive  
and create a new set of corrected files.

The entire archive has been reviewed and remediated with the  
objectives of improving the detailed chemical description of non- 
polymer and monomer chemical components; standardizing atom  
nomenclature; updating sequence database references and taxonomies;  
resolving any remaining differences between chemical and  
macromolecular sequences; improving the representation of viruses;  
and verifying primary citation assignments. In addition, the atom  
nomenclature for amino acids and nucleotides now conforms with IUPAC  

A new FTP server containing the remediated data has been set up for  
testing. The access details for this site are provided at http:// 
www.wwpdb.org/remediation-downloads.html. The new ftp site will be  
updated weekly in concert with the current production site at ftp:// 
ftp.rcsb.org. Both sites share the same directory structure. Starting  
May 1, the remediated data will be served using gzip compression.

Your input is very important to us. PDB users are encouraged to test  
the remediated data files between now and July 2007. The details of  
the final transition will be announced on the wwPDB website (http:// 

Detailed information about the wwPDB remediation project can be found  
at http://remediation.wwpdb.org.

Comments about the files should be sent to info at wwpdb.org. Major  
announcements will be made at the wwPDB website (http:// 
www.wwpdb.org) as well as on the individual member websites.

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