New Features

News

Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive

05/17

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.