PDB Change Advisory Notices

Introduction to Structure Checking by the RCSB

Modifications to established PDB services will be implemented after community review. PDB Advisory Notices are sent out as a means of communicating and refining any changes to the PDB.

These Advisory Notices will be posted on the PDB listserv at least 60 days before any modification is implemented. During a period of public review, we will collect the recommendations and revisions received about the initial notice. A final announcement will be made on the listserv before the change is made.

On July 9, 1999, the RCSB posted its first PDB Change Advisory, which is summarized below. For the full announcement, please see http://www.rcsb.org/pdb/lists/pdb-l/199907/msg00013.html.

Synopsis of PDB Change Advisory Notice (#19990709)

The PDB is fully committed to providing and maintaining the current PDB format in as standard a manner possible; however, as with any standard, there is the occasional need for clarification and amendment. We hope that the changes proposed in this Advisory Notice will be reviewed in the spirit for which they are intended - small changes to an existing mature standard format.

Summary of Proposed Changes:

In short, the changes proposed are:

1. Raise the criteria used in REMARK 500 to flag bond distance and bond angle outliers.
2. Provide improved descriptions for biological assemblies.
3. Standardize the protein hydrogen atom nomenclature following IUPAC recommendations.
4. Permit single PDB ID assignment for NMR ensembles.
5. Provide support for new experimental techniques.
6. Simplify/clarify the specification of macromolecule content within COMPND records.
7. Add new identifying codes for common entry revisions.
8. Obsolete the coden publication identifier.
9. Remove the SEGID field from ATOM, HETATM, SIGUIJ, SIGATM and ANISOU records in the archival format.

The changes proposed here are primarily content changes. Only item 2 above involves a change in the column layout of the PDB file. The remainder of this document provides complete descriptions of each of the proposed changes.

(For a complete description of PDB Change Advisory Notice [#19990709], see http://www.rcsb.org/pdb/lists/pdb-l/199907/msg00013.html.)