Boltz 2 structure and affinity prediction is in ChimeraX daily builds (from July 22, 2025 and later), menu Tools / Structure Prediction / Boltz.  Here's a video showing how to use it looking at the affinity of 5' RNA caps for measles methyltransferase

https://youtu.be/jdoJEcWT-VY

and here is more detailed information about how to make Boltz predictions in ChimeraX

https://www.rbvi.ucsf.edu/chimerax/data/boltz-apr2025/boltz_help.html

Pressing the Options button on the Boltz user interface shows the new option for predicting affinity (image below).

  Tom

boltz2_affinity_option.png

On Jun 30, 2025, at 6:30 PM, Tom Goddard <goddard@sonic.net> wrote:

Hi Saverio,

As Elaine mentioned I am working on having ChimeraX use Boltz 2.1.1 and will put that in the ChimeraX daily build when it is available and will announce it on the mailing list and on BlueSky.  There are currently a bunch of problems with Boltz 2, for instance it won't install on Mac, and might not install on Windows because its installation file (pyproject.toml) says it requires cuequivariance CUDA modules that are only available on Linux.  It is easy to fix that problem, but there are many other problems, errors running on CPU, errors with Mac GPU, prediction quality issues, changed options names (--no_potentials became --use_potentials with opposite default behavior, --no_trifast became --no_kernels).  The Boltz developers are apparently not too interested in making it work on anything but Linux with Nvidia graphics.  But my aim in ChimeraX is that Mac, Windows, and Linux and without Nvidia graphics should all be usable.  I have run tests and been able to fix many of the problems.  Also there is new ChimeraX user interface needed to allow use of the new Boltz 2 capabilities like predicting ligand affinity.  I guess I will have Boltz 2 in ChimeraX daily builds in the latter half of July.

Here is a ChimeraX ticket that describes the many Boltz 2 problems and I will be adding comments as I find fixes

https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/18061

  Tom


On Jun 30, 2025, at 5:49 AM, saverio via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,
it is possible to install the latest version ( 2.1.1 ) of boltz
in ChimeraX 1.10 with the command boltz install?

Thanks.

Saverio


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