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 #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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