Dear all,
At the beginning of October 2023, the Electron Microscopy Data Bank
(EMDB) will start distributing electron microscopy (EM) metadata for its
entries in PDBx/mmCIF file format alongside the already available XML
formatted files.
The addition of PDBx/mmCIF files in the archive will bring parity
between EMDB and PDB (EM experimental data vs 3D structures) in the way
metadata is served while improving the consistency and interoperability
between the two archives. EMDB entries released before October 2023 will
have PDBx/mmCIF files added at a later date.
The description of PDBx/mmCIF categories and items featured in EM
metadata files can be found in the PDBx/mmCIF dictionary
<https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Groups/em_group.html>.
For an EMDB entry EMD-xxxxx, PDBx/mmCIF file name will be
emd-xxxxx.cif.gz and it will be located in the entry's subfolder called
metadata (EMD-xxxxx/metadata) in the wwPDB archive repositories:
* EMDB: https://ftp.ebi.ac.uk/pub/databases/emdb/structures/
* wwPDB: https://files.wwpdb.org/pub/emdb/structures/
* RCSB PDB (US): https://files.rcsb.org/pub/emdb/structures/
* PDBe (UK): https://ftp.ebi.ac.uk/pub/databases/emdb/structures/
* PDBj (Japan): https://files.pdbj.org/pub/emdb/structures/
Read this news online
<http://www.wwpdb.org/news/news?year=2023#651c49e2d78e004e766a96a4>
Kind regards,
Deborah Harrus, on behalf of the wwPDB
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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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