April 2026 - ChimeraX-users - RBVI Mailing Lists

OpenFold Tool Model Selection Question
by Eidman, Zachary M 01 Apr '26

01 Apr '26

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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Boltz Error in ChimeraX on Ubuntu 24 LTS (GPU Workstation)
by Neha Gandhi 01 Apr '26

01 Apr '26

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>

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Issue with SVG export in CircosContacts plugin: Interface residues missing !
by Arun Gupta 01 Apr '26

01 Apr '26

Dear ChimeraX Team, Today I tested the CircosContacts plugin in ChimeraX to generate Circos plots for the peptide–MHC interface. The plugin works as expected in the CircosContacts HTML webpage, where I can see the interface residue/atom contact details between the peptide (Chain Id - C) and MHC chain (Chain Id- A). However, I am not able to observe the interface residues in the exported contacts_circos.svg file. The SVG export appears to be missing the interface residue annotations that are visible in the HTML view. I have attached the exported contacts_circos.svg file for reference. For reproducibility, I used the following command: circoscontacts #1/A restrict #1/C outputDir /Users/arungupta/010426_contacts_1 interModel true intramol false Could you please let me know whether this is expected behavior, or if there is a workaround to ensure that the interface residues are included in the exported SVG file as well or if this is a known limitation of the current version of the plugin ? Thank you for your time and for developing such a useful plugin. Best regards, Arun Arun Gupta PhD, MRSC Sr. Post Doctoral Research Assistant Gillespie/McMichael Group Nuffield Dept. of Clinical Medicine, University of Oxford, Centre for Immuno-Oncology Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ

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