PDB Archive Version 3.15 Released

A newly standardized and enhanced version of the entire PDB archive at ftp://ftp.protein.osaka-u.ac.jp/ and ftp://ftp.wwpdb.org has been released.

Files originally released before December 2, 2008 will follow PDB Format Version 3.15; files originally released after that date will follow Version 3.20. For detailed file format documentation, please see www.wwpdb.org/docs.html.

A time-stamped snapshot of the PDB archive before this release is available from ftp://snapshots.pdbj.org/ and ftp://snapshots.wwpdb.org/ in the directory 20090316.

Users who maintain local copies of the wwPDB FTP will have to download the entire archive. Scripts to help in this process are available at PDBj PDB Archive/Snapshot Archive or http://www.wwpdb.org/downloads.html. For users who make local copies of the wwPDB FTP from PDBj FTP site, please see also News on 2009-01-23.

These data reflect the wwPDB's continuing commitment to providing accurate and detailed data to users worldwide. This release includes improvements and enhancements to the data, including details about the chemistry of the polymer and the ligands bound to it, biological assemblies, and binding sites of ligands and metal ions. An overview (PDF) is provided at the wwPDB website.

Questions may be sent to us or info@wwpdb.org.

Directory structure in PDBj FTP site will be changed

As we described in the Download page, PDBj produces the 20070731 snapshot which is the latest release before the remediation was applied. It is now available from the PDBj snapshot archive. So, we have decided to remove it and will change the directory structure in PDBj FTP as follows:

Before

Current PDB archive

ftp://pdb.protein.osaka-u.ac.jp/ v3/ pub/pdb/

20070731 snapshot (the latest release before remediation)

ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/

After 2009-01-27

Current PDB archive

ftp://pdb.protein.osaka-u.ac.jp/ v3/ pub/pdb/

20070731 snapshot (the latest release before remediation)

ftp://snapshots.pdbj.org/20070731/

And we will reconstruct as the following after the version 3.15 PDB archive will be released:

The version 3.15 PDB archive

ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/

20070731 snapshot (the latest release before remediation)

ftp://snapshots.pdbj.org/20070731/

We will keep ftp://pdb.protein.osaka-u.ac.jp/v3/ as a symbolic link to (updated) ftp://pdb.protein.osaka-u.ac.jp/ in the meantime. But we encourage you to update your services/software to the new directory structure AFTER the change.

We will announce the release date for version 3.15 PDB archive when it will be confirmed.

Sorry for your inconvenience and thank you for your kind understanding.

PDB Archive Version 3.15 to be Released March 18 , 2009

The wwPDB will release a newly standardized and enhanced version of the entire PDB archive at ftp://ftp.protein.osaka-u.ac.jp/ and ftp://ftp.wwpdb.org with the March 18, 2009 update (Japan time).

Files originally released before December 2, 2008 will follow PDB Format Version 3.15; files originally released after that date will follow Version 3.20. For detailed file format documentation, please see www.wwpdb.org/docs.html.

A time-stamped snapshot of the PDB archive before this release will be available from ftp://snapshots.pdbj.org/ and ftp://snapshots.wwpdb.org/.

Users who maintain local copies of the wwPDB FTP will have to download the entire archive. Scripts to help in this process are available at PDBj PDB Archive/Snapshot Archive or http://www.wwpdb.org/downloads.html. For users who make local copies of the wwPDB FTP from PDBj FTP site, please see also News on 2009-01-23.

These data reflect the wwPDB's continuing commitment to providing accurate and detailed data to users worldwide.

Questions may be sent to info@wwpdb.org.

The changes to the wwPDB FTP site has been announced as "The advisory notice" at http://www.wwpdb.org/. (September 25, 2009)

On October 14, 2009, the weekly data update will be made, in principle, at 9:00 AM (JST) of every Wednesday, which corresponds to 0:00 (UTC). This update is simultaneously made at every member of the wwPDB: RCSB-PDB, PDBe, and PDBj.

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On October 14, 2009, we will start to use a new data viewer, PDBj Mine, which has been recently developed by PDBj. Because PDBj Mine uses a relational database, XPath/XQuery is not available. Our XML-based database, xPSSS, is still available for another couple of months.

On November 25, 2009, our existing data viewer xPSSS will be integrated into PDBj Mine, which has recently been developed.

We started using our new data viewer, PDBj Mine, on Oct. 14, 2009. PDBj Mine uses RDB (PostgreSQL), while our exising xPSSS is native XML-based database.

After 9 a.m. Nov.25, 2009, all the accesses to the exising data viewer xPSSS will be automatically switched to jump to PDBj Mine.
Since PDBj Mine is a relational database and cannnot perform a search using XQuery or XPath, xPSSS will still be available, only for the purpose, at http://service.pdbj.org/xPSSS/.

On October 22, 2009, PDBj main pages and deposition pages in " traditional Chinese " have been released.