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We are pleased to announce the availability of PDB versioning, allowing depositors to update their entries while retaining the same PDB accession code.

Depositors can now submit new coordinates for existing entries. Initially, this is limited to PDB entries that were submitted via the OneDep system, which was introduced in 2014. We plan to extend this functionality to entries deposited in the legacy systems (ADIT and Autodep) in future, and will announce a timeline for this in due course.

Requests should be initiated using the OneDep communication panel within the deposition session for the entry in question. Once submitted, the revised model will be processed by wwPDB biocurators and a new version released. Versioning of PDB entries will be limited to changes in the coordinate files, with no changes permitted to the deposited experimental data. PDB versioning will be limited to one replacement per PDB entry per year, and three entries per Principal Investigator per year.

The most recent version of the entry will be available in the main PDB archive FTP (ftp.pdbj.org [PDBj]/ ftp.wwpdb.org [wwPDB]). All major versions of a PDB structure will be retained in the versioned FTP archive (ftp-versioned.pdbj.org [PDBj]/ ftp-versioned.wwpdb.org [wwPDB]) - more information can be found on the wwPDB website. The structure of the versioned FTP archive has been built allowing for future extension of the PDB code format. PDB entry 1abc would therefore be found in the folder pdb_00001abc.

Changes made to entries during versioning are considered to be either “major” or “minor”. Updates to atomic coordinates, polymer sequence, or chemical description trigger a major version increment, while changes to any other categories are indicated as “minor”. Changes introduced are recorded in the PDBx/mmCIF audit categories.

If you have any further queries regarding the process of PDB versioning, please contact the wwPDB at deposit-help@mail.wwpdb.org.

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Created: 2019-08-01 (last edited: 2 weeks ago)2019-08-08