This page is also available in: 日本語

Impact of PDBx/mmCIF v5 upgrade on PDBj services

On July 12 2017, the PDB entries in the FTP will be upgraded to the new v5 dictionary ( http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) (wwPDB News). Since this will be a major upgrade, some services will be affected. The following services will be affected by this upgrade:
Mine 2 RDB Because all entries have been modified, the weekly delta file would be huge and will for that reason NOT be provided on the 12th. The delta files from the previous weeks will also no longer be included on the FTP. Delta files will be included again in the following week onwards (19th). Users will have to delete the current contents of the RDB and then download and load the full dump file, as described on the RDB help page.
Legacy PDBj Mine Legacy PDBj Mine will no longer be updated after the transition of the PDBx/mmCIF dictionary from version 4 (v4) to version 5 (v5) planned on July 12, 2017. After this date, please use the new interface for PDBj Mine that will be compatible with the v5 data. The legacy PDBj Mine will be closed at the end of August, 2017.
2017-06-21
This page is also available in: 日本語
5 Easy Steps to PDB Deposition (wwPDB News)
2017-06-07
This page is also available in: 日本語
Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive (wwPDB News)
2017-05-19 (last edited: 1 month ago)2017-05-22
This page is also available in: 日本語
Enriched PDB Structure Entry Files Conforming to OneDep Data Standards Are Now Available for Testing (wwPDB News)
2017-05-03 (last edited: 1 month ago)2017-05-08
This page is also available in: 日本語
Freezing the PDB Format (wwPDB News)
2017-04-27 (last edited: 1 month ago)2017-04-27
This page is also available in: 日本語

The schema of the PDBj Mine 2 RDB was upgraded to pdbx-v42-v4.069.

On 2017-04-19 the schema of the PDBj Mine 2 RDB was upgraded to pdbx-v42-v4.069, adding support for new tables such as pdbx_deposit_group, enabling searching for group deposition IDs either via the omni search, advanced search or the SQL search.

Similarly, the dump files of the RDB on the FTP have also been updated. In case you experience any issues updating your local RDB with the delta file, please use the full dump file to upgrade the RDB as described on the RDB help page.
2017-04-19 (last edited: 3 months ago)2017-04-19
This page is also available in: 日本語
Archival PDBx/mmCIF Version V4 to V5 Update in the Protein Data Bank (wwPDB News)
2017-03-23
This page is also available in: 日本語
Updated Validation Reports for Archived PDB Structures Now Available (wwPDB News)
2017-03-16 (last edited: 4 months ago)2017-03-17
This page is also available in: 日本語
Data Management: A global coalition to sustain core data (wwPDB News)
2017-03-15 (last edited: 4 months ago)2017-03-15
This page is also available in: 日本語
The paper describing wwPDB OneDep system is now available (wwPDB News)
2017-02-10
This page is also available in: 日本語
Time-stamped Copies of the PDB Archive Available (wwPDB News)
2017-01-12
PDBj@FacebookPDBj@TwitterwwPDBwwPDB FoundationEM DataBank

Copyright © 2013-2017 Protein Data Bank Japan