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News on 2014-12-3

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The jV 4.4.2 is now released. Although there is no change in function, the signature is updated. The certificate used for signing to jV 4.4.1 will expire on 21th Dec. 2014, so you need update the jV to 4.4.2 if you use jV as applet. For stand alone jV, this update is not necessary. http://pdbj.org/jv/index.html#download

Created: 2014-12-18 (last edited: more than 1 year ago)2014-12-18

Integration of Large Structures with the Main PDB Archive ( wwPDB News )

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Integration of Large Structures with the Main PDB Archive (wwPDB News)

Created: 2014-12-10 (last edited: more than 1 year ago)2014-12-11

News on 2014-11-26

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Beginning at January 27, 2015 crystal structures should be submitted using the wwPDB Deposition Tool. ADIT will continue to accept depositions from other experimental methods.

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.


Created: 2014-11-26 (last edited: more than 1 year ago)2014-11-26

Inclusion of Large Structures in the Main PDB Archive ( wwPDB News )

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Inclusion of Large Structures in the Main PDB Archive (wwPDB News)

Created: 2014-09-22 (last edited: more than 1 year ago)2014-09-22

PDBj has released a new service 'Chemie search' and a modified 'search bar' .

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PDBj has released a new service 'Chemie search'.
And the 'search bar' is modified and allows you to more quickly find the resource or service you're looking for.


Created: 2014-09-05 (last edited: more than 1 year ago)2014-09-09

wwPDB Events at IUCr (August 5-12) ( wwPDB News )

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wwPDB Events at IUCr (August 5-12) (wwPDB News)

Created: 2014-08-04 (last edited: more than 1 year ago)2014-08-04

We has frozen the PDBMLplus on PDBj FTP site.

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As announced previously, PDBMLplus files provided from PDBj ftp site has been frozen on 9 July, and will not be updated. Alternatively, you can use the interface in PDBj Mine, which generates it on demand from now on as follows;

Created: 2014-07-18 (last edited: more than 1 year ago)2014-07-18

News on 2014-7-9

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Large Structures has been released" /> Improved Representation of Large Structures in the PDB Archive (wwPDB News)

Created: 2014-07-11 (last edited: more than 1 year ago)2014-07-11

PDB Reaches a New Milestone: 100,000+ Entries ( wwPDB News )

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PDB Reaches a New Milestone: 100,000+ Entries (wwPDB News)

Created: 2014-05-14 (last edited: more than 1 year ago)2014-05-14

The Road to 100,000 Entries: Launching Tools for the Next Generation ( wwPDB News )

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The Road to 100,000 Entries: Launching Tools for the Next Generation (wwPDB News)

Created: 2014-05-07 (last edited: more than 1 year ago)2014-05-07

The Road to 100,000 Entries: The Early Structures ( wwPDB News )

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The Road to 100,000 Entries: The Early Structures (wwPDB News)

Created: 2014-05-02 (last edited: more than 1 year ago)2016-10-05

The Road to 100,000 Entries: Building a Community Resource ( wwPDB News )

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The Road to 100,000 Entries: Building a Community Resource (wwPDB News)

Created: 2014-04-24 (last edited: more than 1 year ago)2014-05-02

We'll finish to provide the PDBMLplus from FTP site. The default URL of PDBMLplus was changed in jV version 4.4 for this change.

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We'll finish to provide the PDBMLplus from FTP site

We are providing the PDBMLplus, which is created by adding extra information collected by PDBj into PDBML-noatom (canonical PDB data file with XML format without atom coordinates), in following two manners.
As we need to hold the same data duplicately by providing the former way, we plan to finish providing merged file (PDBMLplus) from FTP site. After that, we continue to provide the PDBMLadd files which include only additional part from FTP site. For PDBMLplus, you can use the latter interface which generates it on demand. Please use this from now on.
You can also access the PDBMLadd files. e.g.: ftp://ftp.pdbj.org/XML/pdbmlplus/pdbml_add/100d-add.xml.gz.
Although the date to eliminate the PDBMLplus from FTP site isn't decided, we'll announce later when it is decided.
Moreover, the default URL of PDBMLplus was changed in jV version 4.4. So we recommend for all jV users to update jV to this version.

Created: 2014-04-24 (last edited: more than 1 year ago)2014-05-14

The jV 4.4 was released. As the default URL of PDBMLplus file was changed. So we recommend for all jV users to update jV to this version.

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The jV 4.4 was released

We announce the new version of jV (jV 4.4) was released. In this version, load/save function of mmCIF format file and biological unit was implemented. And the default URL of PDBMLplus file was changed. So we recommend for all jV users to update jV to this version.
You can download it from here. The online document is available from here.

Created: 2014-04-24 (last edited: more than 1 year ago)2014-05-14

A fasta file for all the sequence information is now available from the PDBj ftp site.

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In addition to fasta sequence information ('fasta_seq_data/PDBID_seq.txt') for each PDB entry, a fasta file for all the sequence information ('all_fasta_sequence.txt.gz') is now available from the PDBj ftp site.

Created: 2014-04-10 (last edited: more than 1 year ago)2014-04-10

wwPDB X-ray validation reports added to PDB archive ( wwPDB News )

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wwPDB X-ray validation reports added to PDB archive (wwPDB News)

Created: 2014-03-19 (last edited: more than 1 year ago)2014-03-19

Mine2 RDB (Mine 2 Relational DataBase) was released from FTP site on Wednesday, March 5, 2014. For more details, please refer to the help page .

This page is also available in: 日本語
Mine2 RDB (Mine 2 Relational DataBase) was released from FTP site on Wednesday, March 5, 2014. For more details, please refer to the help page.

Created: 2014-03-10 (last edited: more than 1 year ago)2014-03-10

Archiving Structures Derived from SAS Data ( wwPDB News )

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Archiving Structures Derived from SAS Data (wwPDB News)

Created: 2014-02-04 (last edited: more than 1 year ago)2014-02-04

New wwPDB Deposition System Now Available for X-ray Structures ( wwPDB News )

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New wwPDB Deposition System Now Available for X-ray Structures (wwPDB News)

Created: 2014-01-28 (last edited: more than 1 year ago)2014-01-28

Coming soon: X-ray Validation Reports for Archived PDB Structures ( wwPDB News )

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Coming soon: X-ray Validation Reports for Archived PDB Structures (wwPDB News)

Created: 2014-01-17 (last edited: more than 1 year ago)2014-01-17

wwPDB Partners Prepare to Launch New Deposition System ( wwPDB News )

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wwPDB Partners Prepare to Launch New Deposition System (wwPDB News)

Created: 2014-01-10 (last edited: more than 1 year ago)2014-01-10

Announcement: Standardization of Amino Acid Nomenclature ( wwPDB News )

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Announcement: Standardization of Amino Acid Nomenclature (wwPDB News)

Created: 2014-01-10 (last edited: more than 1 year ago)2014-01-10

Download the wwPDB calendar for IYCr:2014 ( wwPDB News )

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Download the wwPDB calendar for IYCr:2014 (wwPDB News)

Created: 2014-01-06 (last edited: more than 1 year ago)2014-01-10

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