Dear CCP4BB,
wwPDB, in collaboration with the PDBx/mmCIF Working Group
<wwpdb.org/task/mmcif>, has set plans
<https://www.wwpdb.org/news/news?year=2021#607760112786e73a79c76f9d> to
extend the length of ID codes for PDB and Chemical Component Dictionary
(CCD) ID entries in the future. These extended formats are not supported
by the legacy PDB file format.
As announced previously
<https://www.wwpdb.org/news/news?year=2017#5910c8d8d3b1d333029d4ea8>,
wwPDB has extended PDB ID length to eight characters prefixed by ‘PDB’,
e.g., pdb_00001abc.
Each PDB ID is issued a corresponding Digital Object Identifier (DOI),
often required for manuscript submission to journals and described in
publications by the structure authors.
To help depositors provide information to journals, OneDep now displays
the PDB ID and DOI on the submission confirmation page.
The extended PDB IDs and corresponding PDB DOIs, along with existing
four character PDB IDs, are now included in the PDBx/mmCIF formatted
files. Initially, this will only be available for updated and
newly-released PDB entries, with an archive-wide update at a later date.
The additional accessions will be provided in the _database_2 PDBx/mmCIF
category.
For example, PDB entry 1ABC will have the extended PDB ID (pdb_00001abc)
and the corresponding PDB DOI (10.2210/pdb1abc/pdb).
loop_
_database_2.database_id
_database_2.database_code
_database_2.pdbx_database_accession
_database_2.pdbx_DOI
PDB 1abc pdb_00001abc 10.2210/pdb1abc/pdb
WWPDB D_1xxxxxxxxx ? ?
Once all available four-character PDB IDs have been consumed,
newly-deposited PDB entries will only be issued extended PDB ID codes.
These entries will only be distributed in PDBx/mmCIF format.
wwPDB asks journals, users, and software developers to review code and
remove related limitations.
Kind Regards,
David Armstrong
--
David Armstrong
Outreach and Training Coordinator
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492544
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