[3dem] ls-lR index file to be removed July 12, 2023

[Justin Flatt]

With continuing growth of the PDB archive, the size of the file that 
lists all directory contents (currently 
https://urldefense.com/v3/__https://files.wwpdb.org/pub/pdb/ls-lR__;!!Mih3wA!FhpAEyO0OuJXuhLhXRpEzQDiCg1eNy3IY-WmP7CC_vhfx2M9KlUBqjybBz0N-QQ_xOni-ucs2O9Ppc340uHzcQpN$ ) will become a challenge for long 
term maintenance. wwPDB will remove this file from the PDB archive at 
00:00 UTC on July 12, 2023. We strongly encourage users to utilize files 
previously announced [1] that containing the same data 
(https://urldefense.com/v3/__https://files.wwpdb.org/pub/pdb/holdings/__;!!Mih3wA!FhpAEyO0OuJXuhLhXRpEzQDiCg1eNy3IY-WmP7CC_vhfx2M9KlUBqjybBz0N-QQ_xOni-ucs2O9Ppc340h2t-L4N$ ).

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 [2] or 
released_structures_last_modified_dates.json.gz [3] in 
/pub/pdb/holdings/.

Please contact info at wwpdb.org with any questions.



Links:
------
[1] https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2021*613b93b3ef055f03d1f222cf__;Iw!!Mih3wA!FhpAEyO0OuJXuhLhXRpEzQDiCg1eNy3IY-WmP7CC_vhfx2M9KlUBqjybBz0N-QQ_xOni-ucs2O9Ppc340oasIp4Q$ 
[2] https://urldefense.com/v3/__https://s3.rcsb.org/pub/pdb/holdings/current_file_holdings.json.gz__;!!Mih3wA!FhpAEyO0OuJXuhLhXRpEzQDiCg1eNy3IY-WmP7CC_vhfx2M9KlUBqjybBz0N-QQ_xOni-ucs2O9Ppc340lH9uot2$ 
[3] 
https://urldefense.com/v3/__https://s3.rcsb.org/pub/pdb/holdings/released_structures_last_modified_dates.json.gz__;!!Mih3wA!FhpAEyO0OuJXuhLhXRpEzQDiCg1eNy3IY-WmP7CC_vhfx2M9KlUBqjybBz0N-QQ_xOni-ucs2O9Ppc340gZeg0wc$ 
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