When a change is made to PDB format, the format version number, as found in the entry and in this Contents Guide, will be incremented to the next whole number. Changes to the format of PDB coordinate entry files will follow the Format Change Policy presented below and will be detailed in this Contents Guide. Beginning January 1997, the format of all PDB entries will be compliant with the current version of this Contents Guide.
Changes to the Contents Guide will be listed at the beginning in the What's New section and denoted by a fractional increase in the document version number. These changes may be of the following kind.
* Correction of typographical errors.
* Changes to the language for clarity.
* Addition or changes to the examples for better representation of format issues.
* Addition of new rules (these do not change the format but help to clarify the semantics).
* Addition of tokens to specification lists, such as in COMPND and SOURCE records, that are needed to more fully describe the structure and its biological source.
* Enhancements to the refinement and experimental details templates in the REMARK records. These remarks are currently being reviewed by several people in the community, and PDB expects to increase the level of detail archived, such as for NMR studies.
* Addition of new sections that enhance and expand the document (these may include topics such as PDB to mmCIF cross references or insertion of relevant sections from the PDB Deposition Form).
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 (pdb-l@pdb.pdb.bnl.gov) and PDB's Internet sites (WWW, FTP, and Gopher). 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 PDB's Internet sites (WWW, FTP, and Gopher).
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 PDB 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.
The PDB wishes to acknowledge Dr. Gerald Selzer of the National Science Foundation who urged us to formulate this policy.