[3dem] Removal of ls-lR index file from the PDB archive

[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!BGWSIyRbxWfOMaTcBMURR_HO4hfOYhRyVNHTksDG78infvOOUD7CH2x2GzJ2ORQGMFP7IYdtWGPtb-SNT3FQe90S$ ) 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 contain the same data 
(https://urldefense.com/v3/__https://files.wwpdb.org/pub/pdb/holdings/__;!!Mih3wA!BGWSIyRbxWfOMaTcBMURR_HO4hfOYhRyVNHTksDG78infvOOUD7CH2x2GzJ2ORQGMFP7IYdtWGPtb-SNT0GeqH8X$ ).

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

Please contact info at wwpdb.org with any questions.

Links:
------
[1] https://urldefense.com/v3/__https://s3.rcsb.org/pub/pdb/holdings/current_file_holdings.json.gz__;!!Mih3wA!BGWSIyRbxWfOMaTcBMURR_HO4hfOYhRyVNHTksDG78infvOOUD7CH2x2GzJ2ORQGMFP7IYdtWGPtb-SNT9XyJYLH$ 
[2] 
https://urldefense.com/v3/__https://s3.rcsb.org/pub/pdb/holdings/released_structures_last_modified_dates.json.gz__;!!Mih3wA!BGWSIyRbxWfOMaTcBMURR_HO4hfOYhRyVNHTksDG78infvOOUD7CH2x2GzJ2ORQGMFP7IYdtWGPtb-SNT-hwQyEI$ 
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