We start a Molmil service to display eF-site electrostatic molecular surfaces.

NBDC portal. The user can search the wwPDB/RDF data along with other data resources through a SPARQL endpoint. See RDF Portal for NBDC for more details." /> The wwPDB/RDF data are now available from the NBDC portal. The user can search the wwPDB/RDF data along with other data resources through a SPARQL endpoint. See RDF Portal for NBDC for more details.

The static version of the PDBj web pages for old-type browsers has been updated.

New version of jV (4.4.4), fixed the bug involved in the polygon display in Windows, was released.

http://pdbj.org/jv/

The wwPDB Symposium "Integrative Structural Biology with Hybrid Methods" will be held at Osaka University Hall on October 3, 2015 (more...)

Phased PDB Release Process (wwPDB News)

Data correspondences between the PDB and CSD archives now available (wwPDB News)

Hybrid/Integrative Methods Paper Published (wwPDB News)

wwPDB Deposition Tool Replaces ADIT for Crystal Structures

As announced on January 27, 2015, ADIT will be retired on July 19, 2015 for structures determined using X-ray crystallography. Any in-progress ADIT X-ray deposition sessions need to be completed before that time.

wwPDB launched the Deposition Tool for structures determined using X-ray crystallography on January 27, 2014 as part of a new Deposition and Annotation System. Using this system, more than 7,600 structures have been deposited and annotated, and more than 3,500 structures released in the archive.

Features of the new system include use of the PDBx/mmCIF data format, which produces more uniform data; the ability to replace data files pre- and post-deposition; enhanced communication; improved annotation; and geometric and experimental data checking based on recommendations from expert task forces. Detailed information and video tutorials are available.

ADIT will continue to accept depositions from other experimental methods. Deposition tools for NMR and 3DEM are being developed by the wwPDB.

Questions and comments should be sent to info@wwpdb.org.

Data Deposition Information for more details." /> New wwPDB Deposition system is now available at PDBj website. Please see Data Deposition Information for more details.

Phased PDB Release Process (wwPDB News)

PDBj has released the electron density maps in the ccp4 format. The ccp4 formatted file of each entry is downloaded from Electron Density Map page through http protocol. The ccp4 formatted files of all entries that have Electron Density Maps are also downloaded from the PDBj FTP site. Those entries are listed at 'edmap.list' in FTP site.

Changes to the Release Process for PDB Entries (wwPDB News)

Beginning at 9:00 a.m. on January 27, 2015 (JST), ADIT deposition system no longer accepts new submissions of crystal structures. Crystal structures should be submitted using the wwPDB Deposition Tool. ADIT will be available for users to finalize in-progress ADIT X-ray depositions until July 19, 2015. ADIT will continue to accept depositions from other experimental methods, such as NMR or Electron Microscopy.

wwPDB launched the Deposition Tool for structures determined using X-ray crystallography on January 27, 2014 as part of a new Deposition and Annotation System. Using this system, more than 4,200 structures have been deposited and annotated, and >1,700 structures released in the archive.

Features of the new system include use of the PDBx/mmCIF data format, which produces more uniform data; the ability to replace data files pre- and post-deposition; enhanced communication; improved annotation; and geometric and experimental data checking based on recommendations from expert task forces. Detailed information and video tutorials are available.

As a result of this successful release, ADIT has been retired at RCSB PDB and PDBj for new depositions of structures determined from X-ray crystallographic experiments. Existing, in-progress ADIT sessions of X-ray crystallographic structures can be accessed until July 19, 2015.

ADIT will continue to accept depositions from other experimental methods. Deposition tools for NMR and 3DEM are being developed by the wwPDB.

Questions and comments should be sent to info@wwpdb.org.

Beginning at 9:00 a.m. on January 27, 2015 (JST) crystal structures should be submitted using the wwPDB Deposition Tool. ADIT will continue to accept depositions from other experimental methods, such as NMR or Electron Microscopy.

wwPDB launched the Deposition Tool for structures determined using X-ray crystallography on January 27, 2014 as part of the new Deposition and Annotation System. More than 3000 structures have been deposited and annotated using this system, with more than 1200 structures already released in the archive. Improvements to this system are regularly incorporated based on user feedback.

As a result of this successful release, RCSB PDB and PDBj will only accept depositions of structures determined from X-ray crystallographic experiments from the wwPDB Deposition Tool beginning January 27, 2015. At this time, the legacy ADIT deposition system will no longer accept new submissions of crystal structures. In-progress ADIT depositions of X-ray crystallographic structures will be able to access their deposition sessions until July 19, 2015.

ADIT will continue to accept depositions from other experimental methods. Deposition tools for NMR and 3DEM are being developed by the wwPDB.

Features of the new system include use of the PDBx/mmCIF data format, which produces more uniform data; the ability to replace data files pre- and post-deposition; enhanced communication; improved annotation; and geometric and experimental data checking based on recommendations from expert task forces. Detailed information and video tutorials are available.

Questions and comments should be sent to info@wwpdb.org.