Keep your ID: PDB versioning is now available

Versioning now allows depositors to update their coordinates while retaining the same PDB accession code.

Initially, versioning is limited to PDB entries that were submitted via the OneDep system, which was introduced in 2014 (with deposition for 3DEM methods added in 2016). Eventually functionality will be extended to entries deposited in the legacy systems.

Requests are 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 is limited to changes in the coordinate files, with no changes permitted to the deposited experimental data, with 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 (http://ftp.wwpdb.org). All major versions of a PDB structure will be retained in the versioned FTP archive (ftp-versioned.wwpdb.org) - more information can be found on the wwPDB website.

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.

For queries regarding PDB versioning, please contact deposit-help@mail.wwpdb.org.

Source: wwPDB News July 31, 2019