Dear PDB-l.
At current growth rates, we anticipate running out of three-character
Chemical Component IDs by the end of 2023. After this point, the wwPDB
will issue five-character alphanumeric accession codes for CCD IDs in
the OneDep system. To avoid confusion with current four-character PDB
IDs, four-character codes will not be used. Owing to limitations of the
legacy PDB file format, PDB entries containing the new five character ID
codes will only be distributed in PDBx/mmCIF and PDBML formats (see
previous announcement
http://www.wwpdb.org/news/news?year=2023#63ff72ccc031758bf1c30ff7).
In addition, wwPDB has reserved a set of CCD IDs: 01 - 99, DRG, INH, LIG
that will never be used in the PDB. These reserved codes can be used for
new ligands during structure determination so that they can be
identified as new upon deposition and added to the CCD during biocuration.
wwPDB asks users and software developers to review code to remove any
current limitations on CCD ID lengths, and to enable use of PDBx/mmCIF
format files. Example files with extended CCD IDs are available via
GitHub https://github.com/wwPDB/extended-wwPDB-identifier-examples to
assist code revisions. Information about the PDBx/mmCIF dictionary and
file format is provided at mmcif.wwpdb.org https://mmcif.wwpdb.org/.
For any further information please contact us at info@wwpdb.org.
--
Regards,
Jasmine
---==========================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
Email:jasmine@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
---==========================
Dear PDB-l.
At current growth rates, we anticipate running out of three-character
Chemical Component IDs by the end of 2023. After this point, the wwPDB
will issue *five-character alphanumeric accession codes for CCD IDs in
the OneDep system*. To avoid confusion with current four-character PDB
IDs, four-character codes will not be used. Owing to limitations of the
legacy PDB file format, PDB entries containing the new five character ID
codes will only be distributed in PDBx/mmCIF and PDBML formats (see
previous announcement
<http://www.wwpdb.org/news/news?year=2023#63ff72ccc031758bf1c30ff7>).
In addition, wwPDB has reserved a set of CCD IDs: 01 - 99, DRG, INH, LIG
that will never be used in the PDB. These reserved codes can be used for
new ligands during structure determination so that they can be
identified as new upon deposition and added to the CCD during biocuration.
wwPDB asks users and software developers to review code to remove any
current limitations on CCD ID lengths, and to enable use of PDBx/mmCIF
format files. Example files with extended CCD IDs are available via
GitHub <https://github.com/wwPDB/extended-wwPDB-identifier-examples> to
assist code revisions. Information about the PDBx/mmCIF dictionary and
file format is provided at mmcif.wwpdb.org <https://mmcif.wwpdb.org/>.
For any further information please contact us at info@wwpdb.org.
--
Regards,
Jasmine
===========================================================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
Email:jasmine@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===========================================================