Dear all,
ThePDB Beta Archive
<https://www.wwpdb.org/news/news.php?year=2026#69ebcdca1103c56d3f444159>will
replace the current archive July 21, 2027. The PDB Beta Archive
organization supports the transition to extended PDB IDs. Users are
strongly encouraged to start using this new directory structure and
extended PDB IDs now.
“Shortlinks” <https://www.wwpdb.org/ftp/pdb-beta-ftp-sites#dataStCon>are
URLs that can be used for downloading data from the beta archive today
without the need to know or code specific file paths, e.g.,
https://files-beta.wwpdb.org/download/pdb_00001abc.cif.gz
When the PDB Beta Archive becomes the main PDB Archive, shortlink users
will only need to update the domain name for these shortlinks:
https://files.wwpdb.org/download/pdb_00001abc.cif.gz
wwPDB recommends that users with automated workflows adopt shortlinks today.
Example Shortlinks
* https://files-beta.wwpdb.org/download/pdb_00001abc.cif.gz
* https://files-beta.wwpdb.org/download/pdb_00001abc-sf.cif.gz
* https://files-beta.wwpdb.org/download/pdb_00001abc_nmr-data.str.gz
* https://files-beta.wwpdb.org/ligands/download/ATP.cif
* …
Transition Resources
* PDB ID Extension FAQ
<https://www.wwpdb.org/documentation/pdb-id-extension-faq>
* PDB Beta Archive Overview: includes beta archive access, scripts,
shortlink URLs, and other resources
<https://www.wwpdb.org/ftp/pdb-beta-ftp-sites>
* PDBx/mmCIF software resources
<https://mmcif.wwpdb.org/docs/software-resources.html>
* Understanding PDBx/mmCIF format
<https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/beginner%E2%80%99s-guide-to-pdbx-mmcif>
* PDBx/mmCIF User Guide
<https://mmcif.wwpdb.org/docs/user-guide/guide.html>
* PDBx/mmCIF Dictionary <https://mmcif.wwpdb.org/>
* PDB -> PDBx/mmCIF correspondences
<https://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html>
* An online PDBx/mmCIF Editor <https://pdbj.org/cif-editor/>
Kind regards,
Deborah Harrus, on behalf of the wwPDB
--
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Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
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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