Dear CCP4BB
Improved access to small molecule definitions
Individual Chemical Component Dictionary (CCD) and Biologically Interest
molecule Reference Dictionary (BIRD) definitions are now accessible in a
new FTP tree in the PDB archive. In response to user requests, these
individual CCD and BIRD entry files can be found at
/pdb/refdata/chem_comp/ and /pdb/refdata/bird/, respectively with last
character hash as sub-directory.
For example:
/pdb/refdata/chem_comp/C/D8C/D8C.cif
/pdb/refdata/bird/prd/8/PRD_001068.cif
Improved access to information about PDB archive holdings
New inventory data files offer a quick overview of data in the archive.
These files are in the extensible JSON format, and can be found under
the new /pdb/holdings/ FTP tree.
The inventory lists provided include:
all_removed_entries.json.gz: list of removed PDB entries (obsolete,
models) with entry authors, entry title, release date, obsolete date ,
and superseding PDB ID, if any.
current_file_holdings.json.gz: List of released PDB entries and file
types present for each entry in the PDB Core Archive (e.g., coordinate
data, experimental data, validation report, ...)
obsolete_structures_last_modified_dates.json.gz: List of obsolete PDB
entries with last time of PDBx/mmCIF file modification
refdata_id_list.json.gz: List of released chemical reference entries,
content types (e.g., Chemical Component, BIRD), and last time of
reference file modification
released_structures_last_modified_dates.json.gz: List of released PDB
entries with last time of PDBx/mmCIF file modification
unreleased_entries.json.gz: List of on-hold PDB entries, entry status,
deposition date, and sequence pre-release information
The inventory (index) files historically provided in /pdb/derived_data/
will continue to be updated for the time being; they will eventually be
removed from the PDB archive. Users are encouraged to utilize these new
inventory files.
Regards
John
--
John Berrisford
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529
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