Individual Chemical Component Dictionary entries and new archive
inventory lists are now available for download
Improved access to small molecule definitions
Individual Chemical Component Dictionary (CCD) and Biologically Interest
molecule Reference Dictionary (BIRD) definitions are now accessible in a
new FTP tree in the PDB archive. In response to user requests, these
individual CCD and BIRD entry files can be found at
/pdb/refdata/chem_comp/ and /pdb/refdata/bird/, respectively with last
character hash as sub-directory.
For example:
-
/pdb/refdata/chem_comp/C/D8C/D8C.cif
-
/pdb/refdata/bird/prd/8/PRD_001068.cif
Improved access to information about PDB archive holdings
New 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/ FTP tree.
The inventory lists provided include:
- all_removed_entries.json.gz: list of removed PDB entries (obsolete,
models) with entry authors, entry title, release date, obsolete date
, and superseding PDB ID, if any.
- current_file_holdings.json.gz: List of released PDB entries and file
types present for each entry in the PDB Core Archive (e.g.,
coordinate data, experimental data, validation report, ...)
- obsolete_structures_last_modified_dates.json.gz: List of obsolete
PDB entries with last time of PDBx/mmCIF file modification
- refdata_id_list.json.gz: List of released chemical reference
entries, content types (e.g., Chemical Component, BIRD), and last
time of reference file modification
- released_structures_last_modified_dates.json.gz: List of released
PDB entries with last time of PDBx/mmCIF file modification
- unreleased_entries.json.gz: List of on-hold PDB entries, entry
status, deposition date, and sequence pre-release information
The inventory (index) files historically provided in /pdb/derived_data/
will continue to be updated for the time being; they will eventually be
removed from the PDB archive. Users are encouraged to utilize these new
inventory files.
https://www.wwpdb.org/news/news?year=2021#top
--
Regards,
Jasmine
---==========================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
Email: jasmine@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
---==========================
Individual Chemical Component Dictionary entries and new archive
inventory lists are now available for download
Improved access to small molecule definitions
Individual Chemical Component Dictionary (CCD) and Biologically Interest
molecule Reference Dictionary (BIRD) definitions are now accessible in a
new FTP tree in the PDB archive. In response to user requests, these
individual CCD and BIRD entry files can be found at
/pdb/refdata/chem_comp/ and /pdb/refdata/bird/, respectively with last
character hash as sub-directory.
For example:
* /pdb/refdata/chem_comp/C/D8C/D8C.cif
* /pdb/refdata/bird/prd/8/PRD_001068.cif
Improved access to information about PDB archive holdings
New 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/ FTP tree.
The inventory lists provided include:
* all_removed_entries.json.gz: list of removed PDB entries (obsolete,
models) with entry authors, entry title, release date, obsolete date
, and superseding PDB ID, if any.
* current_file_holdings.json.gz: List of released PDB entries and file
types present for each entry in the PDB Core Archive (e.g.,
coordinate data, experimental data, validation report, ...)
* obsolete_structures_last_modified_dates.json.gz: List of obsolete
PDB entries with last time of PDBx/mmCIF file modification
* refdata_id_list.json.gz: List of released chemical reference
entries, content types (e.g., Chemical Component, BIRD), and last
time of reference file modification
* released_structures_last_modified_dates.json.gz: List of released
PDB entries with last time of PDBx/mmCIF file modification
* unreleased_entries.json.gz: List of on-hold PDB entries, entry
status, deposition date, and sequence pre-release information
The inventory (index) files historically provided in /pdb/derived_data/
will continue to be updated for the time being; they will eventually be
removed from the PDB archive. Users are encouraged to utilize these new
inventory files.
<https://www.wwpdb.org/news/news?year=2021#top>
--
Regards,
Jasmine
===========================================================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
Email: jasmine@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===========================================================