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PDBj (Protein Data Bank Japan) maintains a centralized archive of macromolecular structures and provides integrated tools, in collaboration with the RCSB, the BMRB in USA and the PDBe in EU. PDBj is supported by JST-BIRD.
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News (on 19 Aug., 2010): Validation Report PDFs wwPDB members provide depositors with detailed reports that include the results of geometric and experimental data checking as part of the structure annotation process. These documents are available from all wwPDB annotation sites as PDF files so that they may be easily reviewed and shared by depositors. As these PDB validation reports provide an assessment of structure quality while keeping the coordinate file confidential, we encourage journal editors and referees to request them from depositors as part of the manuscript submission and review process. The reports are date-stamped, and display the wwPDB processing site logo. They contain essentially the same information, regardless of PDB annotation site (Example reports: RCSB PDB | PDBe | PDBj). The validation reports will continue to be developed and improved as we receive recommendations from our Validation Task Forces for X-ray, NMR, EM, and small angle scattering methods, and as we further develop our data deposition and processing procedures. PDB validation reports are already required by the International Union of Crystallography (IUCr) journals as part of their submission process and are described in an editorial recently published in Nature Structural & Molecular Biology. Questions about these reports and the annotation process may be sent to PDBj or info@wwpdb.org. News (on 13 Jul., 2010): News (on 13 Jun., 2010): News (on 19 May., 2010): News (on 7 May., 2010): News (on 6 May., 2010): wwPDB To Provide Validation Reports as PDFs As part of the structure annotation process, wwPDB members provide depositors with detailed reports that include the results of geometric and experimental data checking. Beginning May 17, 2010 these documents will be available from all wwPDB annotation sites as PDF files so that they may be easily reviewed and shared by depositors. As these PDB validation reports provide an assessment of structure quality while keeping the coordinate file confidential, we encourage journal editors and referees to request them from depositors as part of the manuscript submission and review process. PDB validation reports are already required by the International Union of Crystallography (IUCr) journals as part of their submission process (see Baker et al. (2010) Acta Cryst. F66: 112). The reports are date-stamped, and display the wwPDB processing site logo. They contain essentially the same information, regardless of PDB annotation site. The validation reports will continue to be developed and improved as we receive recommendations from our Validation Task Forces for X-ray, NMR, EM, and small angle scattering methods, and as we further develop our data deposition and processing procedures. Questions about these reports and the annotation process may be sent to us or info@wwpdb.org. News (on 6 May., 2010): Version 2 NMR Restraint Files to be Released in the wwPDB FTP on June 30, 2010With the June 30, 2010 update, a new set of NMR restraint data files will be added to the wwPDB FTP archive (ftp://ftp.wwpdb.org, ftp://ftp.ebi.ac.uk, and ftp://pdb.protein.osaka-u.ac.jp). These restraint files, which will be identified as Version 2 files, are represented in NMR-STAR 3.1 format, contain current PDB atom nomenclature, and provide accurate atom-level correspondences to the NMR model coordinate files in the current wwPDB archive. Restraint files containing restraint data as originally deposited (Version 1 files) will remain on the site and will continue to be updated regularly as new NMR entries are released. About Version 2 Restraint Files The Version 2 NMR restraint files were generated for the wwPDB by the BMRB in collaboration with PDBe and the Centre for Molecular and Biomolecular Informatics/Institute for Molecules and Materials at the Radboud University Nijmegen. NMR restraints were parsed from their original format (Version 1), and harmonized with the coordinates using the software packages Wattos (BMRB and CMBI/IMM), FormatConverter and NMRStarExport (PDBe), and the CCPN framework. The complexity of this process may have lead to minor modifications or loss of data in the Version 2 restraint files due to parsing or conversion errors. The PDB coordinate file and the Version 1 restraint files remain the primary reference for these data. More information about the process used to generate these files is available (1-3). Changes to wwPDB FTP Server The initial release of the Version 2 NMR restraint files will add approximately 5625 new files (310 Mbytes) to the wwPDB FTP site. Version 2 restraint files for new PDB entries will be processed and made available after the PDB entry has been released. Version 1 restraint files for new PDB entries will continue to be released weekly. NMR restraint files are named using extension .mr, as in "1abc.mr.gz" for PDB ID 1abc. Version 2 restraint files will be named "1abc_mr.str.gz", where "str" identifies the NMR-STAR (V3.1) data format. All restraint files are compressed (.gz) using the GNU gzip program.
Version 2 restraint files will be stored in a new directory path, grouped by the middle two characters of the 4-character PDB ID:
All of these data files will be symbolically linked to a single directory: Version 1 restraint files will remain in their current directory structure. For questions, please contact us or info@wwpdb.org. References
News (on 24 Nov., 2009): 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. News (on 22 Oct., 2009): News (on 9 Oct., 2009): News (on 9 Oct., 2009): News (on 25 Sep., 2009): News (on 18 Mar., 2009): 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://pdbjsnap.protein.osaka-u.ac.jp/ 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. News (on 13 Feb., 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://pdbjsnap.protein.osaka-u.ac.jp/ 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. News (on 23 Jan., 2009): 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
After 2009-01-27
And we will reconstruct as the following after the version 3.15 PDB archive will be released:
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. News (on 8 Dec., 2008): A new standardized version of the PDB archive will be available from ftp://ftp.protein.osaka-u.ac.jp/ and ftp://ftp.wwpdb.org in early 2009. All entries released prior to December 2, 2008 will be re-released as PDB Format Version 3.15 files. This release will overwrite all existing files. A snapshot of the archive before this release will be available from ftp://pdbjsnap.protein.osaka-u.ac.jp/ and ftp://snapshots.wwpdb.org/. For documentation, please see www.wwpdb.org/docs.html. Questions may be sent to info@wwpdb.org. News (on 25 Nov., 2008): Beginning December 2, 2008, all newly-released PDB entries will follow PDB File Format Contents Guide Version 3.20 (PDF | HTML). This format includes site and assembly annotation, and supports the nomenclature introduced in 2007 in the Chemical Component Dictionary. The Version 3.20 Changes Guide (PDF) highlights the changes in format from 3.1. Please send any questions to info@wwpdb.org. News (on 16 Sep., 2008): During the past year, the wwPDB annotators have collaborated on a project to clarify the details and procedures related to data processing and annotation. The result is a PDB Contents Guide Version 3.2 that more fully describes the PDB file format. This document is available as a PDF and in HTML, and is accompanied by a document highlighting these clarifications. In the coming months, all files released by the wwPDB will follow the format as described in this document. Details will be made available on this website and at www.wwpdb.org.
News (on 2 Apr., 2008): Data download service via rsync is started. We have started to provide remediated PDB archive via rsync protocol. Rsync is a software which synchronizes files and directories from one location to another while minimizing data transfer using delta encoding when appropriate. Detailed information for PDB archive service is available from PDB archive web page.
News (on 12 Dec., 2007): These data must be deposited at a member site of the Worldwide Protein Data Bank (www.wwpdb.org): PDBj (www.pdbj.org), RCSB PDB (www.pdb.org), PDBe (www.ebi.ac.uk/msd), or BMRB (www.bmrb.wisc.edu). Data can be released as soon as they have been processed and approved. There is a one-year limit on the length of time a structure and its experimental data can be put on hold, including structures that are on hold until the associated paper is published (HPUB). This policy was developed as a result of comments and recommendations from the PDB user community, including the Commission on Biological Macromolecules of the International Union of Crystallography and the NMR Task Force, and has been endorsed by the wwPDB Advisory Committee.
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