Hi Jim, The AlphaFold database fetch in ChimeraX uses an https query to the EBI database as you've seen. It does not have any provision to get the file from local disk. Most ChimeraX users do not have a copy of the 200 million AlphaFold database structures locally, but I understand why GSK wants that. If your local copy of AlphaFold database is accessible via https within your company I could tell you how to make ChimeraX use it. If your copy is just a bunch of files on a file system, I could also tell you how to modify a couple lines of ChimeraX Pythoin code to use those files. Or you could just use the ChimeraX open command to open the AlphaFold database file (e.g. "open /path/to/AFDB/files/AF-P26039-F1-model_v4.cif"). The AlphaFold database Search capability runs using a web service at UC San Francisco that we wrote to do a fast k-mer search of the 200 million sequences. I'm sure you don't have that at GSK. It requires a custom built sequence k-mer database. It also is only designed to run as a REST web service and would probably be a good bit of trouble for you to setup at GSK. Tom
On Oct 9, 2024, at 3:10 AM, Jim Thorpe via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi ChimeraX Team
In our commercial lab we are unable to access public domain AlphaFold databases, and instead have our own copy on-premises. Is there a mechanism to reconfigure the ChimeraX AlphaFold “Fetch” and “Search” features to query our in-house copy?
ChimeraX error reported is: Fetching url https://alphafold.ebi.ac.uk/files/AF-Q5STB3-F1-model_v4.cif failed: HTTP Error 403: Forbidden
Many Thanks for advising me
Best Regards
Jim
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Jim Thorpe Scientific Investigator Protein, Cellular & Structural Sciences Target Discovery
GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK
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