- ChimeraX-users - RBVI Mailing Lists

OpenFold Tool Model Selection Question
by Eidman, Zachary M 02 Apr '26

02 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 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>

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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

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Question about multiple sequence alignment after structural superimposition in ChimeraX
by OLIVA MIGUEL, BALDOMERO 31 Mar '26

31 Mar '26

Dear ChimeraX Team and Community, First, I would like to apologize if my question is redundant. I have only recently joined the community and may have missed previous discussions on this topic. I have been a user of Chimera on macOS, but with the most recent macOS updates, I have encountered compatibility issues that have led me to transition to ChimeraX. I am currently adapting to the new interface and commands, and I appreciate the many improvements it offers. However, I am missing a feature that I frequently used in Chimera: the ability to obtain a multiple sequence alignment after superimposing several structures using MatchMaker. This functionality was very useful in my workflow. I would like to ask whether there is an alternative approach in ChimeraX to achieve this, or if there are plans to include similar functionality in future updates. Thank you very much for your time and assistance. Baldo Oliva -- -- --------------------------- e-mail:baldo.oliva@ <e-mail%3Abaldo.oliva(a)gmail.com>upf.edu Baldo Oliva Miguel, PhD Structural Bioinformatics Laboratory (GRIB-IMIM) Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine (PRBB) C/ Doctor Aiguader, 80. Barcelona-08003, Catalonia, Spain (EU) Tfn: 34-933160509 Fax: 34-933160550

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color the inside of ribbon helix differently
by Daniel Larsson 30 Mar '26

30 Mar '26

Hi ChimeraX team, I would like to color the inside of alpha helices in a different color from the outside, which is a standard feature in PyMOL and the original Chimera program: https://pymolwiki.org/Cartoon_highlight_color https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribinsidecolor.html But my understanding is that this is not currently possible in ChimeraX. I found some old mailing list threads on the topic and this 5-year-old open feature request ticket with priority set to low: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu… https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/1719 Based on comments from the developers, it seems as if implementing this feature is not very straight-forward with the current ribbon rendering engine. Still, I hope you will elevate the priority and put it on the road-map for future releases as it greatly improves visibility and 3D-feeling of large ribbon-style protein structures. It would add another important tool for users of your excellent software. Best regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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ChopChopMF — official user guide now available
by Lukas Bauer 30 Mar '26

30 Mar '26

Dear ChimeraX community, An official user guide for ChopChopMF is now available. ChopChopMF is a ChimeraX plugin designed to streamline protein structure analysis — providing a GUI-based workflow for mapping sequence alignments, mutations, and protein-protein interfaces directly onto 3D structures, without requiring extensive command-line expertise. The user guide covers installation, usage, and practical workflows: https://lukasinscience.github.io/ChopChopMF/ The plugin can be installed directly from the ChimeraX Toolshed: https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxchopchopmf Feedback and suggestions are very welcome. Best regards, Lukas

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Question about clipping and transparency
by John Watters 30 Mar '26

30 Mar '26

Hello All, I am experiencing an issue when I am trying to make a movie of a series of coupled atomic models and volumes overlaid on top of each other. I cannot seem to make what I believe is called the "surface cap" transparent when I have clipped into a volume and I am showing/changing the volume. When I call the transparency command in ChimeraX itself (without the script running) it works as it should and makes the surface cap transparent, but in the movie-making script it seems like the transparency command is having no effect? Do you have any suggestions on how to deal with this? Thank you! Example .cxc code block attempt clip off; clip near -24.984; transparency #1.1 90; ######################### hide #!*.*; hide #!* models; show #!1.2 models; #show volume show #!3 models; #show atomic model transparency #1.2 90;transparency #1.2.1.1 90; wait 3 hide #!*.*; hide #!* models; show #!1.3 models; show #!4 models; transparency #1.3 90;transparency #1.3.1.1 90; wait 3 ######################### Best, John

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How to generate an alignment to color by conservation
by Victor Ruiz-Arroyo 25 Mar '26

25 Mar '26

Dear ChimeraX staff, I am trying to make a representation to display the conservation using a color scale similar to this tutorial: https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-… I have downloaded ~500 target proteins using blast, downloaded the results, and aligned them in clusta omega, which gave me this file: [image: image.png] However everytime I try to open it in chimeraX I get this matrix-like window: [image: image.png] Which is different to what I would expect based on the tutorial. In fact, if I download the .ali from the tutorial, I see the correct alignment window. I have tried different alignment formats without success, and I still get the "matrix window". What software and format do you recommend using in Chimerax? Best Victor

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chimerax-trimmings update
by Oliver Clarke 25 Mar '26

25 Mar '26

Hi all, For anyone using chimerax-trimmings, I gave it a bit of an update: https://github.com/olibclarke/chimerax-trimmings/ I reorganized it and cleaned it up, added more documentation, and took advantage of the new "synopsis" option for aliases to add a help strinng for each alias, so you can access usage info from the command line (typing help or usage followed by the alias name). I also added function keys to toggle shown models on and off, and to toggle shown maps on and off, as well as function keys to cycle through lighting presets, and a function key to cycle through model display options. Hope they are useful to some folks, let me know if so! Cheers Oli

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Color PAE plot from structure
by Pim Huis in 't Veld 19 Mar '26

19 Mar '26

Dear ChimeraX team, I am colouring a PAE plot from a predicted multiprotein structure. From: https://www.cgl.ucsf.edu/chimerax/docs/user/tools/alphafold.html *Color plot from structure – color the plot to match the 3D structure where the pair of entities represented by an X,Y point have the same ribbon color; show the rest of the plot in shades of gray* I would like to use the correct values of the *shades of grey* to make a legend for the plot. Is there a way to see these? Is it possible to include the used palette info on the page above (as for rainbow and green)? Ideally, I would also like to change these shades of grey to have something a bit "steeper" (for example: 0 black, dark grey 5, grey 10, light grey 15, white 30). Is this already possible, or can it be added as a new palette or -ideally- as a customisable feature? Thanks a million! Pim

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