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

05/16 wwPDB News

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. At 00:00 UTC on July 12, 2023, wwPDB will remove the following files from the PDB archive:

  • ../pdb/ls-lR
  • ../pdb/data/structures/ls-lR
  • ../pdb/data/structures/models/ls-lR
  • ../pdb/data/structures/models/current/ls-lR
  • ../pdb/data/structures/models/obsolete/ls-lR

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. Two new inventory files for experimental data are added. 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 [email protected] with any questions.

Updated May 30, 2023

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