This is excellent news - we have a series of related structures solved in the YSBL - several sets of which are on different crystallographic origins. It doesnt matter of course crystallographically but is confusing for comparison.. Now we can alter them to a common origin with redepositing the information.. Eleanor Dodson
On 18 May 2017 at 15:22, Jasmine Young <jas...@rcsb.rutgers.edu> wrote: > Hi Ed, > > The PDB accession code will be based on the primary data stored in the > PDB. Therefore depositors will need to make a new deposition with new PDB > accession code issued if the atomic coordinates are modified using newly > processed intensities from the original diffraction images. > > More details on the procedure will be made available at a later date. > > > Regards, > > Jasmine > > =========================================================== > Jasmine Young, Ph.D. > Biocuration Team Lead > RCSB Protein Data Bank > Associate Research Professor > Center for Integrative Proteomics Research > Rutgers, The State University of New Jersey > 174 Frelinghuysen Rd > Piscataway, NJ 08854-8087 > > Email: jasm...@rcsb.rutgers.edu > Phone: (848)445-0103 ext 4920 > Fax: (732)445-4320 > =========================================================== > > On 5/17/17 12:11 PM, Edward A. Berry wrote: > >> Couple of wuestions: >> What is the procedure for updating an entry? Start a new submission, or >> mail revised coordinates along with an explanation of changes to >> deposit@rcsb? >> >> "unchanged experimental data" - does this mean the exact same structure >> factors, or will newly reduced data from the same original diffraction >> images be acceptable? >> >> Thanks, >> Ed >> >> On 05/17/2017 09:28 AM, Jasmine Young wrote: >> >>> *Use CAUTION opening attachments or clicking on links in emails - IMT >>> Help Desk, 4-4115* >>> >>> >>> >>> The wwPDB is planning to introduce in 2017 a new procedure for the >>> management by the Depositor of Record (where the Depositor of Record is >>> defined as the Principal Investigator for the entry) of substantial >>> revisions to previously released PDB archival entries. >>> >>> At present, revised atomic coordinates for an existing released PDB >>> entry are assigned a new accession code, and the prior entry is obsoleted. >>> This long-standing wwPDB policy had the unintended consequence of breaking >>> connections with publications and usage of the prior set of atomic >>> coordinates, resulting in a non-trivial barrier to submission of atomic >>> coordinate revisions by our Depositors of Record. >>> >>> The wwPDB is introducing a file versioning system that allows Depositors >>> of Record to update their own previously released entries. Please note, in >>> the first phase, file versioning will be applied to the atomic coordinates >>> refined versus unchanged experimental data. >>> >>> Version numbers of each PDB archive entry will be designated using a #-# >>> identifier. The first digit specifies the major version, and the second >>> designates the minor version. The Structure of Record (i.e., the initial >>> set of released atomic coordinates) is designated as Version 1-0. >>> Thereafter, the major version digit is incremented with each substantial >>> revision of a given entry (e.g., Version 2-0, when the atomic coordinates >>> are replaced for the first time by the Depositor of Record). “Major version >>> changes” are defined as updates to the atomic coordinates, polymer >>> sequence(s), and/or chemical identify of a ligand. All other changes are >>> defined as “minor changes”. When a major change is made, the minor version >>> number is reset to 0 (e.g., 1-0 to 1-1 to 2-0). For the avoidance of doubt, >>> the wwPDB will retain all major versions with the latest minor versions of >>> an entry within the PDB archive. >>> >>> Current wwPDB policies governing the deposition of independently refined >>> structures based on the data generated by a research group or laboratory >>> separate from that of the Depositor of Record remain unchanged. Versioning >>> of atomic coordinates will be strictly limited to substitutions made by the >>> Depositor of Record. >>> >>> Upon introduction of the file versioning system, the wwPDB will revise >>> each PDB accession code by extending its length and prepending “PDB” (e.g., >>> "1abc" will become "pdb_00001abc"). This process will enable text mining >>> detection of PDB entries in the published literature and allow for more >>> informative and transparent delivery of revised data files. For example, >>> the atomic coordinates for the second major version of PDB entry 1abc would >>> have the following form under the new file-naming schema: >>> >>> pdb_00001abc_xyz_v2-0.cif.gz >>> >>> The wwPDB is mindful of the importance of continuity in providing >>> services and supporting User activities. For as long as practicable, the >>> wwPDB will continue assigning PDB codes that can be truncated losslessly to >>> the current four-character style. In the same spirit, initial >>> implementation of entry file versioning will appear in a new, parallel >>> branch of the PDB archive FTP tree. More details on the new FTP tree >>> organization and accessibility of version information will be forthcoming. >>> Data files in the current archive location >>> ftp://ftp.wwpdb.org/pub/pdb/data/structures/ will continue to use the >>> familiar naming style and will contain the latest version in the >>> corresponding versioned archive. >>> >>> >>> <http://www.wwpdb.org/news/news?year=2017#top> >>> >>> -- >>> Regards, >>> >>> Jasmine >>> >>> =========================================================== >>> Jasmine Young, Ph.D. >>> Biocuration Team Lead >>> RCSB Protein Data Bank >>> Associate Research Professor >>> Center for Integrative Proteomics Research >>> Rutgers, The State University of New Jersey >>> 174 Frelinghuysen Rd >>> Piscataway, NJ 08854-8087 >>> >>> Email:jasm...@rcsb.rutgers.edu >>> Phone: (848)445-0103 ext 4920 >>> Fax: (732)445-4320 >>> =========================================================== >>> >>>
