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.
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.
- Comments and suggestions will be solicited from the community on specific
problems and data representation issues as they arise.
- Proposed format changes will be disseminated through the PDB Listserver. They
will also be summarized in the PDB Quarterly Newsletter.
- 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.
- 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.
- 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.
- 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
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.