[wwPDB] ls-lR index file to be removed July 12, 2023

With continuing growth of the PDB archive, the size of the file that lists all directory contents (currently https://files.wwpdb.org/pub/pdb/ls-lR) will become a challenge for long term maintenance. wwPDB plans to remove this file from the PDB archive at 00:00 UTC on July 12, 2023. We strongly encourage users to utilize files previously announced that containing the same data (https://files.wwpdb.org/pub/pdb/holdings/).

These 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/ archive tree.

The inventory lists provided include:

• current_file_holdings.json.gz: a list of released PDB entries and the file types present for each in the PDB Core Archive (e.g. coordinate data, experimental data, validation report).
• refdata_id_list.json.gz: a list of released chemical reference entries, their content types (e.g., Chemical Component, BIRD), and the most recent modification date of the reference file.
• released_structures_last_modified_dates.json.gz: a list of released PDB entries with the most recent modification date of the PDBx/mmCIF file.
• released_experimental_data_last_modified_dates.json.gz: a list of released experimental data files with the most recent modification date
• obsolete_structures_last_modified_dates.json.gz: a list of obsoleted PDB entries with the most recent modification date of the PDBx/mmCIF file.
• obsolete_experimental_data_last_modified_dates.json.gz: a list of obsoleted experimental data files with the most recent modification date.
• all_removed_entries.json.gz: a list of obsoleted PDB entries including information for entry authors, entry title, release date, obsolete date, and superseding PDB ID, if any.
• unreleased_entries.json.gz: a list of on-hold PDB entries, their entry status, deposition date, and pre-release sequence information, where available.

Users are encouraged to utilize these inventory files. For example, checking for the update of the PDB archive can be performed using current_file_holdings.json.gz or released_structures_last_modified_dates.json.gz in /pub/pdb/holdings/.

Please contact info@wwpdb.org with any questions.

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