Dear PDB-l,
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:
* 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.
* 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).
* obsolete_structures_last_modified_dates.json.gz: a list of obsoleted
PDB entries with information about the most recent modification
date of the PDBx/mmCIF file.
* 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.
* 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
<https://s3.rcsb.org/pub/pdb/holdings/current_file_holdings.json.gz> or
released_structures_last_modified_dates.json.gz
<https://s3.rcsb.org/pub/pdb/holdings/released_structures_last_modified_dates.json.gz>
in /pub/pdb/holdings/.
Please contact i...@wwpdb.org with any questions.
--
David Armstrong
Outreach and Training Lead
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
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