[3dem] ls-lR index file to be removed July 12, 2023
Justin Flatt
justin at rcsb.rutgers.edu
Wed May 17 10:34:42 PDT 2023
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$
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20230517/37e5950e/attachment.html>
More information about the 3dem
mailing list