News on 2012-09-20
- pdb.protein.osaka-u.ac.jp -> ftp.pdbj.org
- snapshots.pdbj.org -> snapshots.pdbj.org
The ftp command will connect to an anonymous ftp server at PDBj.
ftp ftp.pdbj.org
The following is the new URLs to download various PDB or EMDB data using FTP. Please refer to PDB Archive page for more information.
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PDB Exchange Format (mmCIF):
ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/mmCIF/
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PDBML format (all):
ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/XML/
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PDBML format (no-atom):
ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/XML-noatom/
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PDBML format (ext-atom):
ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/XML-extatom/
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PDB format:
ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/pdb/
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EMDB data:
ftp://ftp.pdbj.org/pub/emdb/structures
The CCP4 workshop was held in Fukuoka on November 2, 2012. The presentation materials are available for download.
The videos for wwPDB Foundation Outreach Seminar, which was held in Osaka on October 13, have been released on YouTube
Announcement: Experimental Data Release Policy Clarification
Effective February 6, 2013, coordinates and experimental data deposited in the PDB will follow the same release status. ( wwPDB News... )
Questions should be sent to info@wwpdb.org.
New Reference Dictionary for Biologically Interesting Molecules (BIRD) Released on FTP
As previously announced, BIRD has been released on the PDBj/wwPDB FTP server at the following sites.
For more details about BIRD, please see the news of Oct 19.
ftp://ftp.pdbj.org/pub/pdb/data/bird/prd/ (PDBj FTP site) ftp://ftp.wwpdb.org/pub/pdb/data/bird/prd/ (wwPDB FTP site)
EMDB header format to be updated to v.1.9.0
On 16 January 2013, the EMDB archive plans to adopt an updated format, v.1.9.0, for the entry header file (XML file associated with each map). This means that EMDB header files distributed from wwPDB partner sites will conform to the 1.9.0 format, and EMDataBank deposition/annotation/search services will start using this format.
We are announcing this planned change in advance so that developers can make any necessary modifications to software/services that make use of EMDB header files. Please contact us at help@emdatabank.org with any questions or concerns.
The candidate schema is available for download here:
ftp://ftp.pdbj.org/pub/emdb/doc/XML-schemas/Header-schema/candidate/emdb.xsd
.
A complete list of changes can be found at the beginning of the schema file.
Example header files using the new format can be found here:
ftp://ftp.pdbj.org/pub/emdb/examples1.9.0.
For more details about the schema change, see wwPDB News.
Remediation of Structure Factor Data and Release Plan
The wwPDB has reviewed structure factor files in the archive for format consistency and correspondence with coordinate data. As a result, around 43,800 structure factor files have been updated to standardize the format and to incorporate data corrections. Changes made are described in the audit.details record of the structure factor file.
Starting January 16, 2013, the wwPDB will begin to release these modified structure factors in weekly batches of 1000. These files will be available from ftp://ftp.pdbj.org/pub/pdb/data/structures/all/structure_factors/.
Questions should be sent to info@wwpdb.org.
News on 2012-10-17
News on 2012-10-19
The wwPDB has reviewed the representation of peptide-like antibiotic and inhibitor molecules in the PDB archive. As a result, a new reference dictionary has been created to help define and represent these biologically interesting molecules.
This Biologically Interesting molecule Reference Dictionary (BIRD) contains chemical descriptions, sequence and linkage information, and functional and classification information as taken from the core structures and from external resources. PDB entries containing these molecules will be annotated using this dictionary, and will contain a corresponding BIRD ID code only in the PDBx-formatted file.
BIRD will be available on the wwPDB FTP server adjacent to the Chemical Component Dictionary.
The use of BIRD will greatly improve the consistency of peptide-like antibiotic and inhibitor molecules in the PDB.
These data reflect the wwPDB's continuing commitment to providing accurate and detailed data to users worldwide.
Nobel Prize Awarded for studies of G-protein-coupled receptors
The 2012 Nobel Prize in Chemistry was awarded jointly to Robert J. Lefkowitz and Brian K. Kobilka for studies of G-protein-coupled receptors. The PDB holds many GPCRs, such as Kobilka's groundbreaking structure of the2 adrenergic receptor-Gs protein complex ( 3sn6 ).
Learn more about this award and related structures at PDBe and RCSB PDB. PDBj also provides eProtS articles about2 adrenergic receptor (eProtS: 2rh1 and 3p0g ).
News on 2012-03-07
The EM Data Bank (EMDB) has joined the PDB archive on March 7, 2012. Now it is available from PDBj ftp site at ftp://pdb.protein.osaka-u.ac.jp/pub/emdb. ( wwPDB News... )
News on 2012-10-04
PDBj has been providing RDF(Resource Description Framework)-formatted PDB data based on the pdbj.org domain. From now on, the URLs of PDB/RDF data will be provided from the rdf.wwpdb.org domain.
The following are examples of the change.
- http://pdbj.org/rdf/1GOF -> http://rdf.wwpdb.org/pdb/1GOF
- http://pdbj.org/chem_comp/ATP -> http://rdf.wwpdb.org/cc/ATP
