March 2026 - ChimeraX-users - RBVI Mailing Lists

MCP for ChimeraX
by Alexis Rohou 20 Oct '26

20 Oct '26

Hi all, I would like to use ChimeraX via an agent. Quick googling suggests I'm not the first person to think of this (here <https://github.com/chatmol/molecule-mcp>, here <https://github.com/GDAmitha/chimerax-alphafold-mcp>), but before I dive in I thought I'd check - anyone else actively working on this? Or maybe you have worked on it and hit a roadblock? Cheers, Alexis

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clip
by Timothy Springer 10 Aug '26

10 Aug '26

Can you translate this into a clip command I can use in a .cxc file? clip list Using 2 clip planes: near offset -3.0783, axis -0.462,-0.880,0.109, point on plane 218.1,184.5,202.4) far offset 12.676, axis 0.462,0.880,-0.109, point on plane 210.8,170.6,204.1) - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

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cartoon style setting
by junjie han 07 Aug '26

07 Aug '26

Hi, May I ask how I can set the cartoon thick for a specific region of a structure in ChimeraX? For instance, the command "cartoon style #1/A:10-20 thick" plays an effect on the whole #1 molecule, not only affecting the specific region #1/A:10-20. Please let me know what the appropriate command is by any chance. Thanks, Junjie

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Suggestion
by Samo Lešnik 23 Apr '26

23 Apr '26

Dear developers, I have a small suggestion: if the residue name is detected as HOH, TIP3, WAT, ... (whatever the list of waters are), then the bond between H2 and H1 is not drawn, as this is an artifact of the small distance. Best regards, Samo

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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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