Hi David,

  Thanks for the AlphaFold training video.  Through much of 2025 I was working on making Boltz, an AlphaFold 3 spin off, easier to use in ChimeraX by allowing you to run it on your Mac or Windows machine.  AlphaFold 3 (and 2) require Linux.  Also the MSA calculation of AlphaFold requires large databases and a lot of CPU power.  So I suspect with AF3 beginner users can only use Google's AF3 server.  And of course there is the no-commercial-use licensing, and inability to run arbitrary ligands on Google's server.  For all these reasons I have felt Boltz (MIT license) running on your local computer is a better option for most academic biology researchers.  So I hope to nudge you in that direction!  In the past month I also made it relatively easy to run Boltz predictions from your Mac or Windows computer on a Linux/Nvidia system if you have one available to make larger and faster predictions (https://www.rbvi.ucsf.edu/chimerax/data/boltz-apr2025/boltz_server.html).

  I haven't watched your video yet.  I've made ChimeraX videos about how to use Boltz on YouTube and am disatisfied with all the ads.  I probably could get a youtube ad blocker or paid account but have not and suspect many of the biology researchers have not.  So I've long been considering putting all my ChimeraX videos on Vimeo so they can be viewed ad-free.   I admit I started watching your video but in a minute got a long unskippable ad and gave up.

Tom


On Jan 3, 2026, at 8:00 AM, David S. Fay via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Everyone,

Despite not really being qualified, I’ve done several protein modeling workshops at universities over the past year with some positive responses. It seems to be quite useful to a good number of scientists like myself (clueless molecular/cellular biologists etc), and in particular for less experienced users. Part of my ability to pull this off at any level has been the help I’ve received from others including the wonderful staff the ChimeraX, who I give ample props to in the video. 

Anyway, feel free to share with students or others who might find this useful. It’s rather long (97 minutes) and I do go into a fair bit of detail about how ipTM is determined along with some of the recently developed alternative metrics for scoring protein-protein interactions. I’ve attached the link below. I also realize that this user group is very sophisticated, so feel free to comment or correct and to add to anything I may have missed or not stated properly.

Thanks and happy new year,

David

David S. Fay Ph.D.
Professor, Department of Molecular Biology
Director (PD/PI), National Institutes of Health Wyoming INBRE
University of Wyoming
email: davidfay@uwyo.edu


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