Question about openfold command line syntax
Hi, I couldn’t find documentation regarding the correct syntax for running multiple models and using different seeds from the ChimeraX openfold platform. I tried something similar to what has worked for boltz: openfold predict #1/A #1/B recycle 3 seed 3 samples 5, but got an error (Expected a keyword). Tried a few other iterations but came up empty. Thanks in advance. David Fay
Hi David, For the command documentation, use ChimeraX command "help openfold" or see the copy on our website: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/openfold.html#predict> Maybe you want the "samples" and "seed" options. There isn't a "recycle" option. Also you may need to get a recent daily build, as the openfold interface and associated command were added after the latest production release. 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 Apr 26, 2026, at 7:38 PM, David S. Fay via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I couldn’t find documentation regarding the correct syntax for running multiple models and using different seeds from the ChimeraX openfold platform. I tried something similar to what has worked for boltz: openfold predict #1/A #1/B recycle 3 seed 3 samples 5, but got an error (Expected a keyword). Tried a few other iterations but came up empty.
Thanks in advance.
David Fay
Hi David, The ChimeraX Log highlights where the problem is when you type a command with invalid arguments. For instance, your OpenFold prediction commands shows openfold predict <https://www.rbvi.ucsf.edu/chimerax/data/openfold-feb2026/openfold.html> #1/A #1/B recycle 3 seed 3 samples 5 Expected a keyword The red background starting at the "recycle" option and the "Expected a keyword" message means that "recycle" is not an option. The ChimeraX openfold command that Elaine mentioned lists all the options. OpenFold 3 is based on AlphaFold 3 and so internally it does a number of recycles but that parameter is not currently exposed via ChimeraX. The default number of recycles is 3 in OpenFold 3 and it is not available as an openfold command-line parameters and is set in an OpenFold project file model_config.py. Tom
On Apr 27, 2026, at 8:01 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi David, For the command documentation, use ChimeraX command "help openfold" or see the copy on our website: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/openfold.html#predict>
Maybe you want the "samples" and "seed" options. There isn't a "recycle" option. Also you may need to get a recent daily build, as the openfold interface and associated command were added after the latest production release.
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 Apr 26, 2026, at 7:38 PM, David S. Fay via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I couldn’t find documentation regarding the correct syntax for running multiple models and using different seeds from the ChimeraX openfold platform. I tried something similar to what has worked for boltz: openfold predict #1/A #1/B recycle 3 seed 3 samples 5, but got an error (Expected a keyword). Tried a few other iterations but came up empty.
Thanks in advance.
David Fay
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participants (3)
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David S. Fay -
Elaine Meng -
Tom Goddard