Hi Zach,

  ChimeraX installs and runs predictions with OpenFold 3 preview 2 an implementation of AlphaFold 3.  It does not use OpenFold 2 or OpenFold Multimer which are older programs based on AlphaFold 2.  As far as I know there are no special settings for running multimer predictions in OpenFold 3 or AlphaFold 3.  You specify all of your protein sequences and it will predict the complex.

  More info about ChimeraX OpenFold 3 capabilities can be found here

https://www.rbvi.ucsf.edu/chimerax/data/openfold-feb2026/openfold.html

  Tom


On Apr 1, 2026, at 11:59 AM, Eidman, Zachary M via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I’ve recently started using the OpenFold tool in ChimeraX and I’ve found it really useful so far. I’m trying to model multimeric complexes and I’m wondering if the tool automatically detects multimeric inputs and uses OpenFold Multimer as the model? I noticed in some config files there is code that detects monomeric versus multimeric input, but I don’t see any indication of what model is used in any of my output files. Any input would be greatly appreciated.

Thanks!
Zach Eidman
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