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PDB Format Changes Implemented

Starting November 3, 1999, all files released by the PDB will reflect the changes listed below. A full description and explanation is available in the summary of comments on PDB Change Advisory Notice that was announced on October 13, 1999.

  1. The REMARK 500 outlier criteria will be raised to 6*RMSD to flag bond distance and bond angle outliers.

  2. The changes to the REMARK 300 and 350 templates will provide improved descriptions for biological assemblies.

  3. The protein hydrogen atom nomenclature following IUPAC recommendations will be made available on a separate ftp site.

    After the summary of comments to our Format Change Advisory was posted last week, we received some additional comments on our plans to provide IUPAC-compliant hydrogen atom nomenclature in newly processed files. Accordingly, we have revised our implementation plan for this change.

    We will continue to place files into the PDB archive with the CURRENT hydrogen atom nomenclature. Files with IUPAC-compliant nomenclature will be placed in a separate area on the PDB ftp server. These files will carry new REMARK records that clearly and prominently identify these files as having a IUPAC hydrogen atom nomenclature. Details about the location of the new files will be announced shortly.

  4. The COMPND record will simplify/clarify the specification of macromolecule content.

  5. The REVDAT modification type ("modType") will be used to indicate whether a structure is a re-released Layer 1 entry (with a modification type of 4) or if it is a re-released entry that has been modified as part of the data uniformity project (with a modification type of 5).

    For example, the following REVDAT is for a structure that has been re-released as a Layer 2 file after being initially released as a Layer 1.

    REVDAT 2 03-NOV-99 1ABC 4

    The following REVDAT is for a structure that has been modified as part of the data uniformity project.

    REVDAT 2 03-NOV-99 1BER 5

  6. CODEN identifiers will not be included in files released on or after November 3, 1999.