[3dem] News Update: ls-lR index file in the PDB archive to be removed on July 12, 2023

[Justin Flatt]

Dear 3DEM community,

NEW UPDATE:

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

------------------------------------------------------------------------------------------------

See details at 
https://urldefense.com/v3/__http://www.wwpdb.org/news/news?year=2023*645bbfdd1d621d75127a7a48__;Iw!!Mih3wA!Bqpzxzi7NOzfp8QcLnjg-EqA0xD8PIGFrOmEC8vcA6-NG72nV4YdB5qEWOoiQgz3V67sYreTzzOAS7tWUx2z_atw$ 

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!Bqpzxzi7NOzfp8QcLnjg-EqA0xD8PIGFrOmEC8vcA6-NG72nV4YdB5qEWOoiQgz3V67sYreTzzOAS7tWUz_JjyB9$ ) 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 
<https://urldefense.com/v3/__http://www.wwpdb.org/news/news?year=2021*613b93b3ef055f03d1f222cf__;Iw!!Mih3wA!Bqpzxzi7NOzfp8QcLnjg-EqA0xD8PIGFrOmEC8vcA6-NG72nV4YdB5qEWOoiQgz3V67sYreTzzOAS7tWUzBmexhS$ > [1] 
that containing the same data 
(https://urldefense.com/v3/__https://files.wwpdb.org/pub/pdb/holdings/__;!!Mih3wA!Bqpzxzi7NOzfp8QcLnjg-EqA0xD8PIGFrOmEC8vcA6-NG72nV4YdB5qEWOoiQgz3V67sYreTzzOAS7tWU30ILUH-$ ).

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 
<https://urldefense.com/v3/__https://s3.rcsb.org/pub/pdb/holdings/current_file_holdings.json.gz__;!!Mih3wA!Bqpzxzi7NOzfp8QcLnjg-EqA0xD8PIGFrOmEC8vcA6-NG72nV4YdB5qEWOoiQgz3V67sYreTzzOAS7tWU7J5kJth$ > [2] 
or released_structures_last_modified_dates.json.gz 
<https://urldefense.com/v3/__https://s3.rcsb.org/pub/pdb/holdings/released_structures_last_modified_dates.json.gz__;!!Mih3wA!Bqpzxzi7NOzfp8QcLnjg-EqA0xD8PIGFrOmEC8vcA6-NG72nV4YdB5qEWOoiQgz3V67sYreTzzOAS7tWU7zfWCJd$ > 
[3] in /pub/pdb/holdings/.

Please contact info at wwpdb.org with any questions.

/Updated May 30, 2023/



Links:
------
[1] https://urldefense.com/v3/__http://www.wwpdb.org/news/news?year=2021*613b93b3ef055f03d1f222cf__;Iw!!Mih3wA!Bqpzxzi7NOzfp8QcLnjg-EqA0xD8PIGFrOmEC8vcA6-NG72nV4YdB5qEWOoiQgz3V67sYreTzzOAS7tWUzBmexhS$ 
[2] https://urldefense.com/v3/__https://s3.rcsb.org/pub/pdb/holdings/current_file_holdings.json.gz__;!!Mih3wA!Bqpzxzi7NOzfp8QcLnjg-EqA0xD8PIGFrOmEC8vcA6-NG72nV4YdB5qEWOoiQgz3V67sYreTzzOAS7tWU7J5kJth$ 
[3] 
https://urldefense.com/v3/__https://s3.rcsb.org/pub/pdb/holdings/released_structures_last_modified_dates.json.gz__;!!Mih3wA!Bqpzxzi7NOzfp8QcLnjg-EqA0xD8PIGFrOmEC8vcA6-NG72nV4YdB5qEWOoiQgz3V67sYreTzzOAS7tWU7zfWCJd$ 
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