Dear all,
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
http://www.wwpdb.org/news/news?year=2023#645bbfdd1d621d75127a7a48
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. 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
<http://www.wwpdb.org/news/news?year=2021#613b93b3ef055f03d1f222cf> 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. 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://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.
Kind regards,
Deborah Harrus
PDBe
--
-------------------------------------------------------------------
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
http://www.PDBe.org
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