PDB Format Change Policy

The PDB will use the following protocol in making changes to the way PDB coordinate entries are represented and archived. The purpose of the new policy is to allow ample time for everyone to understand these changes and to assess their impact on existing programs. These modifications are necessary to address the changing needs of our users as well as the changing nature of the data that is archived.

  1. Comments and suggestions will be solicited from the community on specific problems and data representation issues as they arise.

  2. Proposed format changes will be disseminated through the PDB Listserver. They will also be summarized in the PDB Quarterly Newsletter.

  3. A sixty-day discussion period will follow the announcement of proposed changes. Comments and suggestions must be received within this time period. Major changes which are not upwardly compatible will be allotted up to twice the standard amount of discussion time.

  4. This sixty-day discussion period will be followed by a thirty-day period in which the PDB staff, the PDB Advisory Board, and the User Group Chair will evaluate and reconcile all suggestions. The final decision pertaining to the format change, which lies with the Advisory Board Chair, will then be officially announced via the PDB Listserver and Bulletin Board.

  5. Implementation will follow official announcement of the format change. Major changes will not appear in PDB files earlier than sixty days after the announcement, allowing sufficient time to modify files and programs.

  6. Changes will be released no more than twice a year, unless extraordinary circumstances require action. This will be done only in consultation with the Advisory Board and following the usual ninety-day discussion and evaluation period.

The PDB format has been in use since the late 1970's. A number of groups including the mmCIF Committee have been looking at ways to upgrade both the file content and the interchange format used by PDB. This is clearly needed due to changes in the data that PDB archives, the size of the database itself, and finally, to allow us to use more up-to-date methods for representing and storing biological data.

The PDB plans to be prudent and deliberate in making changes to the current PDB files in order to minimize the need to change existing programs. In particular, we will explore ways and means of ensuring that programs which read the current ATOM/HETATM records can continue to do so in the foreseeable future.

Finally, we wish to acknowledge Dr. Gerald Selzer of the National Science Foundation who urged us to formulate this policy.