Boltz Error in ChimeraX on Ubuntu 24 LTS (GPU Workstation)
Dear Team, I hope you are doing well. I am writing to report an issue with running Boltz within ChimeraX on my Ubuntu 24 LTS GPU workstation. Until yesterday, Boltz was functioning correctly and I was able to successfully predict protein–ligand binding affinities. However, starting today, the workflow has begun failing with an error (line 125) during execution. I have tried the following troubleshooting steps: - Reinstalled ChimeraX and tested both the daily build and version 1.12 - Verified GPU functionality (other tools such as OpenFold are running without issues) Current behavior: - Boltz successfully predicts ligand-only structures - Boltz successfully predicts protein-only structures - However, it fails when attempting protein–ligand complex predictions. I tried using command line but didn't work. This suggests the issue may be specific to the combined workflow rather than general installation or GPU configuration. Could you please advise on: 1. Possible causes for this error (especially related to recent updates or dependencies)? 2. Any logs or debug steps I should provide? 3. Recommended fixes or configuration changes? I would be happy to share error logs or system details if needed. Thank you for your support. Best regards, Neha Gandhi Get Outlook for Android<https://aka.ms/AAb9ysg>
Hi Neha, Use the "Report Bug" button on the error dialog in ChimeraX when the error occurs. That way I will see your ChimeraX version, graphics driver version, stack trace of all the function calls where the error happened, what commands were executed.... If there is no Report Bug button use ChimeraX menu entry Help / Report a Bug after you get the error. Tom
On Apr 1, 2026, at 7:22 AM, Neha Gandhi via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Team,
I hope you are doing well.
I am writing to report an issue with running Boltz within ChimeraX on my Ubuntu 24 LTS GPU workstation.
Until yesterday, Boltz was functioning correctly and I was able to successfully predict protein–ligand binding affinities. However, starting today, the workflow has begun failing with an error (line 125) during execution.
I have tried the following troubleshooting steps:
- Reinstalled ChimeraX and tested both the daily build and version 1.12 - Verified GPU functionality (other tools such as OpenFold are running without issues)
Current behavior:
- Boltz successfully predicts ligand-only structures - Boltz successfully predicts protein-only structures - However, it fails when attempting protein–ligand complex predictions. I tried using command line but didn't work.
This suggests the issue may be specific to the combined workflow rather than general installation or GPU configuration.
Could you please advise on:
1. Possible causes for this error (especially related to recent updates or dependencies)? 2. Any logs or debug steps I should provide? 3. Recommended fixes or configuration changes?
I would be happy to share error logs or system details if needed.
Thank you for your support.
Best regards, Neha Gandhi
Get Outlook for Android <https://aka.ms/AAb9ysg>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Tom, I reinstalled boltz22. It worked! Cheers, Neha From: Tom Goddard <goddard@sonic.net> Sent: Wednesday, April 1, 2026 10:32 PM To: Neha Gandhi <neha@goldlakelifesciences.com> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Boltz Error in ChimeraX on Ubuntu 24 LTS (GPU Workstation) Hi Neha, Use the "Report Bug" button on the error dialog in ChimeraX when the error occurs. That way I will see your ChimeraX version, graphics driver version, stack trace of all the function calls where the error happened, what commands were executed.... If there is no Report Bug button use ChimeraX menu entry Help / Report a Bug after you get the error. Tom On Apr 1, 2026, at 7:22 AM, Neha Gandhi via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear Team, I hope you are doing well. I am writing to report an issue with running Boltz within ChimeraX on my Ubuntu 24 LTS GPU workstation. Until yesterday, Boltz was functioning correctly and I was able to successfully predict protein–ligand binding affinities. However, starting today, the workflow has begun failing with an error (line 125) during execution. I have tried the following troubleshooting steps: - Reinstalled ChimeraX and tested both the daily build and version 1.12 - Verified GPU functionality (other tools such as OpenFold are running without issues) Current behavior: - Boltz successfully predicts ligand-only structures - Boltz successfully predicts protein-only structures - However, it fails when attempting protein–ligand complex predictions. I tried using command line but didn't work. This suggests the issue may be specific to the combined workflow rather than general installation or GPU configuration. Could you please advise on: 1. Possible causes for this error (especially related to recent updates or dependencies)? 2. Any logs or debug steps I should provide? 3. Recommended fixes or configuration changes? I would be happy to share error logs or system details if needed. Thank you for your support. Best regards, Neha Gandhi Get Outlook for Android<https://aka.ms/AAb9ysg> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
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Neha Gandhi -
Tom Goddard