wwPDB 2009 News
Contents
12/16/2009
Coordinated wwPDB Release of Data
The PDB archive can be accessed at FTP sites at the RCSB PDB, PDBe,
and PDBj. The update schedules for these sites have been coordinated
to be simultaneous. All updates now occur at the target time of
Wednesday 00:00 UTC (Coordinated Universal Time).
There is no change to the timeline for structure release requests. Any author correspondence
required to release a PDB entry should be sent to the appropriate wwPDB member site by 12 noon
local time on Thursdays in order for the entry to be prepared for release. This correspondence
(which can include citation information, responses to outstanding issues, etc.) should be sent to:
After the files are ready, all entries due for release are transferred to the RCSB PDB
for final packaging into the master PDB ftp archive. These files are then released by at
the target time of Wednesday, 00:00 UTC (Coordinated Universal Time).
Requests received after these cutoff times will be processed during the next update cycle.
09/25/2009
wwPDB FTP Advisory Notice
This advisory notice describes four changes to the content of the wwPDB
FTP site. The changes described here will become effective on Nov 24, 2009.
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The script for mirroring the FTP site using the RSYNC program has been updated.
The new script has been modified to prompt the user to choose one of three
rsync servers (RCSB PDB, PDBe, PDBj). The rsync script has the following URLs:
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The top-level README file has been updated to point to an expanded set of
download instructions hosted on the wwPDB website. The URL for the download
instructions is:
wwPDB website: Download Archive - Data Download Instructions
The URLs for the updated README file are located at:
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The directories containing newsletters have been updated.
Newsletters can be found in the following URLs:
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Sequence cluster data that is used only by the RCSB PDB website has been relocated
to an RCSB PDB resource site. This data was formerly located at the following
URLS:
The new URL for this data is:
RCSB PDB: ftp://resources.rcsb.org/sequence/clusters/
06/30/2009
wwPDB News: Gerard Kleywegt to head Protein Data Bank Europe
Starting July 1, 2009, Gerard Kleywegt will lead the Protein Data Bank Europe (PDBe)
project at the European Bioinformatics Institute (Hinxton, UK). During the last 17
years he has been working in Uppsala, Sweden, a center of excellence for biomolecular
crystallography and has developed many tools that are widely used by structural biologists
worldwide. He has an extensive publication record and has served on the PDBe Scientific
Advisory Board for the last few years. He has also been one of the European representatives
on the wwPDB advisory committee. He has a very strong international reputation and is
well respected in the structural biology community.
Gerard will be replacing Kim Henrick, who has been the team leader of the PDBe since 2001.
During his tenure at the EBI, Kim has made enormous contributions to the PDBe at the EBI,
by establishing and leading a strong team that has developed a wide variety of services.
Kim was a strong advocate for the formation of the wwPDB in 2003. He has played a key role
in developing the standards for representing all the data in the archive from small molecules
to very large biological assemblies, and in leading the remediation efforts. Kim's deep
knowledge of the PDB, his very critical eye, and sharp wit will be greatly missed by the wwPDB.
The members of the wwPDB look forward to working closely with Gerard and wish Kim
all the best in the next chapter of his career.
03/17/2009
PDB Archive Version 3.15 Released
A newly standardized and enhanced version of the entire PDB archive at
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 File Format Documentation.
A time-stamped snapshot of the PDB archive before this release is available from
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 Download Archive - Data Download Instructions.
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 [email protected].
03/10/2009
Announcement: PDB Archive Version 3.15 to be Released March 17, 2009*
The wwPDB will release a newly standardized and enhanced version of the entire PDB archive at
ftp://ftp.wwpdb.org with the March 17, 2009 update. *Please note the revised date.
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 File Format Documentation.
A time-stamped snapshot of the PDB archive before this release will be available from
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 Download Archive - Data Download Instructions.
These data reflect the wwPDB's continuing commitment to providing accurate and detailed data to users worldwide.
Questions may be sent to [email protected].
02/11/2009
Announcement: PDB Archive Version 3.15 to be Released March 2009
The wwPDB will release a newly standardized and enhanced version of the entire PDB archive at
ftp://ftp.wwpdb.org in March 2009.
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 File Format Documentation.
A time-stamped snapshot of the PDB archive before this release will be available from
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 Download Archive - Data Download Instructions.
These data reflect the wwPDB's continuing commitment to providing accurate and detailed data to users worldwide.
Questions may be sent to [email protected].
01/28/2009
wwPDB Paper: Deposition and Annotation
wwPDB deposition tools, methods, and policies have been described in
Data Deposition and Annotation at the Worldwide Protein Data Bank Molecular Biotechnology (2008) [
doi:10.1107/S0907444908017393 ]
Shuchismita Dutta, Kyle Burkhardt, Jasmine Young, Ganesh J. Swaminathan, Takanori Matsuura, Kim Henrick, Haruki Nakamura and Helen M. Berman
01/20/2009
Time-stamped Copies of PDB Archive Available via FTP
A time-stamped snapshot of the PDB archive (ftp://ftp.wwpdb.org)
as of January 5, 2009 has been added to ftp://snapshots.rcsb.org/.
Snapshots of the PDB have been archived annually since 2004. It is hoped that these snapshots will
provide readily identifiable data sets for research on the PDB archive.
The script at ftp://snapshots.rcsb.org/rsyncSnapshots.sh
may be used to make a local copy of a snapshot or sections of the snapshot. The directory 20090105 includes
the 55,072 experimentally-determined coordinate files that were current at that time.
Coordinate data are available in PDB, mmCIF, and XML formats.
The date and time stamp of each file indicates the last time the file was modified.
12/18/2008
Advisory Committee Meeting
The Worldwide Protein Data Bank Advisory Committee (wwPDBAC) met in Hinxton on September 29, 2008.
The presentations by wwPDB members and the report from the wwPDBAC are available at
wwPDB Advisory Committee Meetings.