April 2026 - ChimeraX-users - RBVI Mailing Lists

Orbital Viewer - Gaussian formatted checkpoint
by Matthias Bremer 09 Apr '26

09 Apr '26

Dear All, when trying to render molecular orbitals from a Gaussian .fchk file, I get the following error message: WARNING AaronTools.fileIO.FileReader.read_fchk could not create Orbitals, try increasing the max. array size to read from FCHK files I used the 6-31+G(d) basis. How can I fix this? Best regards Matthias Bremer

2 1

vseries movie recording with frame labels
by Rayees Mattoo 07 Apr '26

07 Apr '26

Hi, I want to record a vseries movie, a total of 20 frames (frame 0-19). I used the below script. I want to include a frame label (Frame 0 to 19) as the movie oscillates across frames. The frame numbers should appear in sync with the movie frames. How can I include that and record with vseries? movie record; vseries play #1 direction oscillate loop true; wait 200; movie encode ~/Desktop/vseries_movie1.mp4 Best Rayees

2 2

Visualizing contact sites on structures larger than atoms
by Wilson, Melissa (NIH/NINDS) [F] 03 Apr '26

03 Apr '26

Hello, I am currently using ChimeraX to reconstruct mitochondria undergoing autophagy. I am interested in visualizing contact sites between the mitolysosome, surrounding mitochondria, and endoplasmic reticulum. The clashes/contacts command<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/clashes.html#options> is all in the context of atoms. Can this command be used for the purpose of larger structures? Or is there another method in ChimeraX to achieve such a visualization? All of my models are surfaces. Best, Melissa Wilson

2 1

Issue with SVG export in CircosContacts plugin: Interface residues missing !
by Arun Gupta 03 Apr '26

03 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

4 4

OpenFold Tool Model Selection Question
by Eidman, Zachary M 03 Apr '26

03 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

3 4

Boltz Error in ChimeraX on Ubuntu 24 LTS (GPU Workstation)
by Neha Gandhi 02 Apr '26

02 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>

2 2

addh to only parts of a model?
by Alexis Rohou 01 Apr '26

01 Apr '26

Hi all, As specified in the documentation, in command addh, "Hydrogens are added to entire atomic model(s) even if only parts of models are specified." Given how specifically this is stated, I'm guessing there was a good rationale for doing it this way. However I am facing a situation where I'd really, really like to add hydrogens only to waters (which were added by Servalcat). For reasons that I haven't got to the bottom of, addh adds hydrogens in the wrong places in a ligand I'm working on (a peptide with a mixture of natural and non-canonical amino acids, though I'm almost certain I've observed this behavior with other, less exotic, ligands). So: what is/was the rationale for not allowing users to add hydrogens to only parts of a model? How would the developers feel about a pull request adding an option to override this behavior and only add hydrogens to the spec supplied by the user? Cheers, Alexis

2 1