Dear Colleagues,
PDBe has madePDBx/mmCIF files, containing SIFTS mapping information and
additional, standardised metadata available directly from the EMBL-EBI
FTP area, from:
https://ftp.ebi.ac.uk/pub/databases/msd/updated_mmcif/
PDBe’s release process creates these enriched PDBx/mmCIF files from PDB
archive files, containing more consistent, standardised metadata,
without altering core PDB information, such as atomic coordinates and
experimental data. These PDBx/mmCIF files have recently been further
enriched with data from the SIFTS process
<https://www.ebi.ac.uk/pdbe/about/news/sifts-data-now-included-pdbe-mmcif-files>,
providing improved mapping between structure and sequence data.
These enriched PDBx/mmCIF files are compressed and distributed from two
subfolders in the FTP area. Firstly, you can efficiently access files
for individual entries via the ‘divided’ folder, where each entry is
placed within a folder identified by the second and third characters of
the PDB entry ID (e.g. divided/at/1atp_updated.cif.gz). Alternatively,
all the compressed updated PDBx mmCIF files in the PDB archive are
available from the ‘all’ folder (e.g. all/1atp_updated.cif.gz).
Alternatively, these files can also be downloaded from PDBe entry pages
(https://www.ebi.ac.uk/pdbe/entry-files/download/7o9f_updated.cif).
These files are also accessible via static URL
(https://www.ebi.ac.uk/pdbe/static/entry/7o9f_updated.cif) or via PDBe
bulk download service available at https://www.ebi.ac.uk/pdbe/download/api.
If you have any queries about these files or how to access them, please
contact our helpdesk at [email protected].
Kind Regards,
David Armstrong
--
David Armstrong
Outreach and Training Coordinator
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492544
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