Hi Anna, As Elaine says ChimeraX structure prediction is using ColabFold which is an optimized version of AlphaFold 2. If you want the exact version of ColabFold and AlphaFold being used it is in the ChimeraX code https://github.com/RBVI/ChimeraX/blob/f44f848ce802b3917680327e2383ab183195ff... and it is currently using something close to ColabFold 1.5.5 from Nov 2023 https://github.com/sokrypton/ColabFold/commit/29395e7dee2c2895eaf585ef6b6cde... which appears to use AlphaFold-ColabFold version 2.3.6 (seen in the ColabFold file) https://github.com/sokrypton/ColabFold/blob/main/pyproject.toml ColabFold uses a forked version of Google's AlphaFold project called AlphaFold-ColabFold https://pypi.org/project/alphafold-colabfold/ So the exact versions used are a bit of trouble to track down. At any rate it appears ChimeraX is using the most recent versions (but not AlphaFold 3). Tom
On Aug 9, 2024, at 8:48 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Anna, This is explained in the ChimeraX User Guide, see the help page for the AlphaFold tool -- you can press the "Help" button on that tool or see the copy at our website here:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html>
To summarize,
(1) if you are using search or fetch, it is not running a new calculation but getting a pre-existing model from the AphaFold Database.
(2) if you are using predict to run a new prediction, it is using ColabFold which is an open-source optimized version of AlphaFold 2.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 9, 2024, at 3:19 AM, Anna Mestre Borras via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I would like to confirm which is the AlphaFold version in ChimeraX 1.8 when using Tools --> structure prediction --> AlphaFold.
Thanks! Best, Anna
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