Allow ChimeraX to use a boltz prediction server

[Tom Goddard]

Would like to allow ChimeraX to send prediction input files to a server where the predictions is computed and then returned to ChimeraX. This would allow easily running predictions on low-powered laptops (e.g. MacBook Air) if the user has a more capable system such as a Linux / Nvidia desktop. The server process will also be created by ChimeraX on the server machine and use the Boltz installed by ChimeraX on that machine. The mechanism can send over a socket a zip file of the Boltz input (.yaml, command options, and MSA) and receive back from the server a zip file with the output (stdout, stderr, boltz_results_name).

The aim of this is not that UCSF would provide a server, but instead a user would very easily be able to setup a server on their own computer or on a cloud-based virtual machine.

I hope to try this setup for running predictions with the students in the January 2026 Biophysics Macromolecular Structures course.

[Tom Goddard]

I added a boltz prediction server capability. A ChimeraX command "boltz start server" is used to start the server on one computer. Other computers running ChimeraX can then use a new "User server [host] [port]" option in the ChimeraX boltz gui to run predictions on the server. Details are described here

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

There are also "boltz predict" command options useServer, serverHost, serverPort to run predictions on a server.

Unlike boltz predictions run on the local computer, you can quit ChimeraX after starting a server prediction and later fetch that prediction in a new ChimeraX session. I added a new user interface Boltz History (menu Tools / Structure Prediction, also available from a new button History on the Boltz GUI). It shows a table of all Boltz predictions made using ChimeraX as described here

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

If there are active server predictions (defined as ones that did not complete by the time ChimeraX exited) then a "Fetch from server" button will appear on the Boltz History panel to fetch them. Also the "boltz server list" and "boltz server fetch" commands described in the above boltz server link can be used to list and fetch server predictions.