February 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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An error opening chimerax seesion
by Yehuda Halfon 11 Mar '26

11 Mar '26

Hi all, I'm using chimeraX 0.8 (2018-12-17) on centos 7 (can't remember the build). Sometimes when I load a session that was saved using this version of chimeraX it gives me this error: Unable to restore session, resetting. Traceback (most recent call last): File "/software/graphics/chimerax/lib/python3.6/site-packages/chimerax/core/ session.py", line 593, in restore obj = sm.restore_snapshot(self, data) File "/software/graphics/chimerax/lib/python3.6/site-packages/chimerax/ std_commands/view.py", line 214, in restore_snapshot for k,v in data ['view attrs'].items(): TypeError: 'NoneType' object is not subscriptable After that I can't open the session again, so I need to remake it. Help, Yehuda Halfon

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VR on ubuntu workstation
by arangarajan＠initialtx.com 04 Mar '26

04 Mar '26

Hi, i got steam VR installed but later found out that Oculus does not support linux. Is there a work around for using chimerax VR on latest ubuntu machine with oculus rift s headset? i can get other headset also if it will fit this purpose. thanks in advance, best amith

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ISOLDE and secondary structure restraints
by Guido Hansen 02 Mar '26

02 Mar '26

Hi all, I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess: Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script? Cheers, Guido -- PD Dr. Guido Hansen Group Leader UNIVERSITÄT ZU LÜBECK INSTITUT FÜR BIOCHEMIE Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen(a)biochem.uni-luebeck.de www.biochem.uni-luebeck.de [1] Ratzeburger Allee 160 23562 Lübeck Links: ------ [1] http://www.biochem.uni-luebeck.de

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Help with capping of helices - ribbon style
by Eliane Hadas Yardeni 27 Feb '26

27 Feb '26

Hello, Recently I downloaded the new version of ChimeraX and noticed that in the ribbon style the helices now look hollow. In the older version of chimera, the helices were capped. Is there a way to cap the helices in the new version? Below is an example from the old version and the new version: Old: [cid:1fff36fe-586e-4307-98f3-a2f03b125fde] New: [cid:86e871a6-1c71-4488-9bc3-f1b209a57bec] Thank you for your help. Best, Eliane

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Cannot specify chain ID using /B:300 notation in .defattr file
by Anne-Frances Miller 27 Feb '26

27 Feb '26

Dear All, I can make .defattr files that work well for render-by-attribute, if I specify residues only as :arg or :206 (examples). However if I want to specify a particular residue in a particular chain (e.g. /A:206), I can load a .defattr file with no error, but the attribute is not found by the render-by-attribute or select-by-attribute capabilities. (I did not attempt the retired :206.A notation. Maybe I should ?) Has anyone gotten chain-specific resIDs to work in a .defattr file please? Thank you •—•—•—•—•—•—•—•—•—•—•—•—• A.-F. Miller, Ph. D. (she/elle/sie) Gill Eminent Professor Distinguished Prof. of Arts and Sciences Professor of Chemistry University of Kentucky https://uky.zoom.us/j/3250841836 https://millerlablive.wordpress.com/

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Canno specify chain ID using /B:300 notation in .defattr file
by Anne-Frances Miller 27 Feb '26

27 Feb '26

Dear All, I can make .defattr files that work well for render-by-attribute, if I specify residues only as :arg or :206 (examples). However if I want to specify a particular residue in a particular chain (e.g. /A:206), I can load a .defattr file with no error, but the attribute is not found by the render-by-attribute or select-by-attribute capabilities. (I did not attempt the retired :206.A notation. Maybe I should ?) Has anyone gotten chain-specific resIDs to work in a .defattr file please? Thank you - • - • - • - • - • - • - • - • - A.-F. Miller, Ph. D. (she/elle/sie) Gill Eminent Professor Distinguished Prof. of Arts and Sciences Professor of Chemistry University of Kentucky https://uky.zoom.us/j/3250841836 https://millerlablive.wordpress.com/

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Reproducible image generation
by Guillaume Gaullier 25 Feb '26

25 Feb '26

Hello chimerax-users, I generated images using a command script, which is mostly reproducible on the same computer (so long as I don't change the size of the 3D window between runs). However, when running the script with the same map and model files but on a different computer, I get slightly different images: different dimensions, different aspect ratio. I assemble these images in multi-panel figures in Inkscape, with linked images so the panels automatically update when I regenerate the images from ChimeraX: this is very helpful to quickly iterate changes in display style, colors etc. and see how they look in the multi-panel figure. So I need reproducibility because, if the new images have different dimensions, the objects of interest in these images will move relative to the annotations around them in the multi-panel figure. Even worse, when the aspect ratio of the new image is different, Inkscape forces it into the aspect ratio of the original image that was inserted into the multi-panel figure, so the new image is squished or stretched in one direction. Obvious solution: do it all on the same computer. In this specific case I could do that (and probably will), but what if the first computer was no longer functioning? I'd like to have a solution if this ever happens, and preferably one that doesn't require me to manually fix every single one of the now misplaced vector elements (this almost amounts to making the multi-panel figure from scratch again). I tried two different things to fix this, hoping to get two different computers to produce identical images (same number of pixels in width and height, same centering of the scene), but none seemed to produce completely reproducible results: 1) I ran the "windowsize" command on computer A with the ChimeraX window as I would have it to generate the images (in this case, maximized). Then I wrote this command in the script with the values obtained on computer A, and ran this script on computer B. The image generated on computer B now has the same aspect ratio than the one generated on computer A, but still has different dimensions. I guess this is because the two screens have different pixel densities? This trick also only worked with the ChimeraX window not maximized on computer B, which could be because its screen has more pixels so needs less "screen space" to make the equivalent image size (in pixels) as the one from computer A. 2) In addition to the "windowsize" command, I specified image width and height explicitly in my save command, setting them the same as the dimensions of the image generated on computer A. This is getting closer: the image from computer B now has the same aspect ratio and same dimensions as the image from computer A. But the outlines of "graphics silhouettes true" appear thicker in the new image than in the original. Is there a fully reproducible way to generate images on different computers with different displays? Thank you, Guillaume 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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