PDBe SIFTS Mappings now working again in Jalview [Fixed 2023-01-26]

Jalview Announcements
1

We’ve just discovered that PDB <> Uniprot mappings provided to Jalview by the PDBe’s SIFTS service are currently not being discovered properly.

We expect this to be a temporary issue, but will post a work around in this thread shortly for people who need to have SIFTS mappings in Jalview right now!

2

Workaround:

Jalview stores SIFTS files for each PDB structure in a directory called ‘.sifts_mappings’ usually found in your home directory (e.g. /Users/jalview/.sifts_mappings on OSX).

For a PDB ID like 1xyz, you will find a file ‘1xyz.xml.gz’ in that directory - if it isn’t there, Jalview tries to download it from the EBI. The URL Jalview uses for this is currently not providing all the SIFTS records for the PDB, but you can work around this by downloading the xml.gz file yourself from http://ftp.ebi.ac.uk/pub/databases/msd/sifts/split_xml/xy/1xyz.xml.gz

  • just replace the ‘xy’ after /split_xml/ with the second and third character in the PDB ID, and add ‘.xml.gz’ to the PDB ID at the end to get the URL for the PDB structure you want to view.
3

We’ve just heard from the wonderful people at PDBe that the SIFTS resource that Jalview relies on is now fully up to date.