Improved Access to Chemical Component Definitions and Archive Inventories
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.
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.