Re: [ccp4bb] Formageddon is upon us... Important news from wwPDB! (help-4246)
Dear Robbie, We will continue the practice that any structure deposited as a single PDBx/mmCIF file will be divided into SPLIT files and added to the ftp archive as usual, in all supported formats (PDB, PDBx/mmCIF, PDBML/XML). Entries are split only for reasons of size. SPLIT entries currently in the archive will remain as they are until sometime in 2014 when we plan to consolidate all existing and new SPLIT entries into single large files. Regards, Rachel Rachel Kramer Green, Ph.D. RCSB PDB kra...@rcsb.rutgers.edu Twitter: https://twitter.com/#!/buildmodels Facebook: http://www.facebook.com/RCSBPDB On 5/24/2013 12:41 PM, Robbie Joosten wrote: Perhaps a silly question: will old entries with SPLIT records be superseded by consolidated entries? And what about entries split for other reasons than size (there are only a few of those, and they are old)? Cheers, Robbie Van: Gerard DVD Kleywegt Verzonden: 24-5-2013 20:21 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] Formageddon is upon us... Important news from wwPDB! Dear colleagues, I would like to draw your attention to a notification from the wwPDB partners about Deposition and Release of PDB Entries Containing Large Structures - see: http://www.wwpdb.org/news/news_2013.html#22-May-2013 There are major changes afoot in the way large structures are handled in the PDB, as well as in the deposition and annotation procedures and software used by the wwPDB sites. This is of immediate relevance for depositors and users of large structures, but also for software developers and anyone who routinely processes the entire PDB archive or its weekly releases (bioinformatics resources, etc.). From 2014, it will affect essentially everyone who deposits, uses or processes PDB entries. If you have any questions about the new deposition system or the procedures for handling large structures or any of the other changes, please contact: i...@wwpdb.org Please pass on this information to anyone likely to be affected by the upcoming changes. Thanks! On behalf of the Worldwide Protein Data Bank, --Gerard Kleywegt --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] Formageddon is upon us... Important news from wwPDB! (help-4246)
Hi Rachel, Thanks for clarifying this. Things will be much easier when SPLIT entries are consolidated. That is, when all the software is updated as well. Entries are split only for reasons of size. 1apg was, sort of, an example of the contrary (see the, now obsolete, reflection file). I thought there were more examples, but fortunately I couldn't find any quickly. Cheers, Robbie We will continue the practice that any structure deposited as a single PDBx/mmCIF file will be divided into SPLIT files and added to the ftp archive as usual, in all supported formats (PDB, PDBx/mmCIF, PDBML/XML). Entries are split only for reasons of size. SPLIT entries currently in the archive will remain as they are until sometime in 2014 when we plan to consolidate all existing and new SPLIT entries into single large files. Regards, Rachel Rachel Kramer Green, Ph.D. RCSB PDB kra...@rcsb.rutgers.edu Twitter: https://twitter.com/#!/buildmodels Facebook: http://www.facebook.com/RCSBPDB On 5/24/2013 12:41 PM, Robbie Joosten wrote: Perhaps a silly question: will old entries with SPLIT records be superseded by consolidated entries? And what about entries split for other reasons than size (there are only a few of those, and they are old)? Cheers, Robbie Van: Gerard DVD Kleywegt Verzonden: 24-5-2013 20:21 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] Formageddon is upon us... Important news from wwPDB! Dear colleagues, I would like to draw your attention to a notification from the wwPDB partners about Deposition and Release of PDB Entries Containing Large Structures - see: http://www.wwpdb.org/news/news_2013.html#22-May-2013 There are major changes afoot in the way large structures are handled in the PDB, as well as in the deposition and annotation procedures and software used by the wwPDB sites. This is of immediate relevance for depositors and users of large structures, but also for software developers and anyone who routinely processes the entire PDB archive or its weekly releases (bioinformatics resources, etc.). From 2014, it will affect essentially everyone who deposits, uses or processes PDB entries. If you have any questions about the new deposition system or the procedures for handling large structures or any of the other changes, please contact: i...@wwpdb.org Please pass on this information to anyone likely to be affected by the upcoming changes. Thanks! On behalf of the Worldwide Protein Data Bank, --Gerard Kleywegt --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
[ccp4bb] Formageddon is upon us... Important news from wwPDB!
Dear colleagues, I would like to draw your attention to a notification from the wwPDB partners about Deposition and Release of PDB Entries Containing Large Structures - see: http://www.wwpdb.org/news/news_2013.html#22-May-2013 There are major changes afoot in the way large structures are handled in the PDB, as well as in the deposition and annotation procedures and software used by the wwPDB sites. This is of immediate relevance for depositors and users of large structures, but also for software developers and anyone who routinely processes the entire PDB archive or its weekly releases (bioinformatics resources, etc.). From 2014, it will affect essentially everyone who deposits, uses or processes PDB entries. If you have any questions about the new deposition system or the procedures for handling large structures or any of the other changes, please contact: i...@wwpdb.org Please pass on this information to anyone likely to be affected by the upcoming changes. Thanks! On behalf of the Worldwide Protein Data Bank, --Gerard Kleywegt --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] Formageddon is upon us... Important news from wwPDB!
Perhaps a silly question: will old entries with SPLIT records be superseded by consolidated entries? And what about entries split for other reasons than size (there are only a few of those, and they are old)? Cheers, Robbie Van: Gerard DVD Kleywegt Verzonden: 24-5-2013 20:21 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] Formageddon is upon us... Important news from wwPDB! Dear colleagues, I would like to draw your attention to a notification from the wwPDB partners about Deposition and Release of PDB Entries Containing Large Structures - see: http://www.wwpdb.org/news/news_2013.html#22-May-2013 There are major changes afoot in the way large structures are handled in the PDB, as well as in the deposition and annotation procedures and software used by the wwPDB sites. This is of immediate relevance for depositors and users of large structures, but also for software developers and anyone who routinely processes the entire PDB archive or its weekly releases (bioinformatics resources, etc.). From 2014, it will affect essentially everyone who deposits, uses or processes PDB entries. If you have any questions about the new deposition system or the procedures for handling large structures or any of the other changes, please contact: i...@wwpdb.org Please pass on this information to anyone likely to be affected by the upcoming changes. Thanks! On behalf of the Worldwide Protein Data Bank, --Gerard Kleywegt --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
