[wwPDB] Improved Access to Chemical Component Definitions and Archive Inventories

Improved access to small molecule definitions (New tree: /pdb/refdata/)

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 tree: /pdb/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.

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