February 2026 - ChimeraX-users - RBVI Mailing Lists

ISOLDE and secondary structure restraints
by Guido Hansen 25 Feb '26

25 Feb '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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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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Scenes as in chimera
by Rapisarda, Chiara /FR 25 Feb '26

25 Feb '26

Hello, I would like to make movies as I used to with chimera using scenes so that smooth transitions to show different things can then be tweaked to modify figures if needed. Is it possible with chimeraX? I didn’t see anything about it? I remember there was a thread about saving each scene separately which is what I do as cxs, but I have not seen anything about putting the scenes together to make a movie. Can anybody help, or could this be implemented in chimeraX if it is not available? Also another feature that I miss about chimera is the ability to select a colour palette from colorbrew. I still do that manually, but in Chimera that was a choice in the list and it makes figure making so much easier. Thank you for all the nice work on the tool anyway. Best, Chiara Chiara RAPISARDA Senior Principal Scientist I, Group Head Bio Structure and Biophysics +33 (0)1 58 93 21 95 chiara.rapisarda(a)sanofi.com<mailto:chiara.rapisarda@sanofi.com> 13 quai Jules Guesde, 94400 Vitry S/Seine, France [signature_3187861101]<https://www.sanofi.com/> [signature_825373031]<https://www.facebook.com/sanofi/> [signature_3246108776] <https://www.twitter.com/sanofi/> [signature_579974037] <https://www.linkedin.com/company/sanofi/> [signature_2146776366] <https://www.instagram.com/sanofi/> [signature_2874155821] <https://www.youtube.com/user/sanofiaventistven>

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Volume eraser as cube?
by Oliver Clarke 25 Feb '26

25 Feb '26

Hi all, Hope the chimeraX team & community are having a great start to 2025! There are often situations (in single particle cryo-EM) where I would like to erase using a plane rather than a sphere - e.g., when I want to chop off density protruding from a nanodisc or micelle in order to make a mask. There are various workaround ways to do this (e.g. just making the sphere enormous, making a cubic/rectangular mask and multiplying/substracting, etc), but I was wondering if this is a common enough scenario (perhaps other users can chime in?) that it might be worth adding the option of erasing using a cube rather than a sphere? Cheers Oli

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how to align models to 0,0,0 z axis for saving to PDB ?
by Mitch Murphy 24 Feb '26

24 Feb '26

please help i cant figure out how to align a complicated set of models so the barrell of my hexameric ion channel is aligned along z axis and centered at 0,0,0 to save a pdb close cd /Users/mitch/github/hmx/jahani/egfrv3 log clear # ---------------- tmCLIC1 ---------------- open ../charmmgui-clic1/step1_pdbreader.pdb id 99 center 0,0,0 color :1-23 blue color :24-58 green color :59-241 red torsion :25@c:26@n,ca,c -60; torsion :26@n,ca,c:27@n -45 torsion :26@c:27@n,ca,c -60; torsion :27@n,ca,c:28@n -45 torsion :27@c:28@n,ca,c -60; torsion :28@n,ca,c:29@n -45 torsion :28@c:29@n,ca,c -60; torsion :29@n,ca,c:30@n -45 torsion :29@c:30@n,ca,c -60; torsion :30@n,ca,c:31@n -45 torsion :30@c:31@n,ca,c -60; torsion :31@n,ca,c:32@n -45 torsion :31@c:32@n,ca,c -60; torsion :32@n,ca,c:33@n -45 torsion :32@c:33@n,ca,c -60; torsion :33@n,ca,c:34@n -45 torsion :33@c:34@n,ca,c -60; torsion :34@n,ca,c:35@n -45 torsion :34@c:35@n,ca,c -60; torsion :35@n,ca,c:36@n -45 torsion :35@c:36@n,ca,c -60; torsion :36@n,ca,c:37@n -45 torsion :36@c:37@n,ca,c -60; torsion :37@n,ca,c:38@n -45 torsion :37@c:38@n,ca,c -60; torsion :38@n,ca,c:39@n -45 torsion :38@c:39@n,ca,c -60; torsion :39@n,ca,c:40@n -45 torsion :39@c:40@n,ca,c -60; torsion :40@n,ca,c:41@n -45 torsion :40@c:41@n,ca,c -60; torsion :41@n,ca,c:42@n -45 torsion :41@c:42@n,ca,c -60; torsion :42@n,ca,c:43@n -45 torsion :42@c:43@n,ca,c -60; torsion :43@n,ca,c:44@n -45 torsion :43@c:44@n,ca,c -60; torsion :44@n,ca,c:45@n -45 torsion :44@c:45@n,ca,c -60; torsion :45@n,ca,c:46@n -45 torsion :45@c:46@n,ca,c -60; torsion :46@n,ca,c:47@n -45 torsion :46@c:47@n,ca,c -60; torsion :47@n,ca,c:48@n -45 torsion :47@c:48@n,ca,c -60; torsion :48@n,ca,c:49@n -45 torsion :48@c:49@n,ca,c -60; torsion :49@n,ca,c:50@n -45 torsion :49@c:50@n,ca,c -60; torsion :50@n,ca,c:51@n -45 torsion :50@c:51@n,ca,c -60; torsion :51@n,ca,c:52@n -45 torsion :51@c:52@n,ca,c -60; torsion :52@n,ca,c:53@n -45 torsion :52@c:53@n,ca,c -60; torsion :53@n,ca,c:54@n -45 torsion :53@c:54@n,ca,c -60; torsion :54@n,ca,c:55@n -45 torsion :54@c:55@n,ca,c -60; torsion :55@n,ca,c:56@n -45 torsion :55@c:56@n,ca,c -60; torsion :56@n,ca,c:57@n -45 torsion :56@c:57@n,ca,c -60; torsion :57@n,ca,c:58@n -45 torsion :57@c:58@n,ca,c -60; torsion :58@n,ca,c:59@n -45 torsion :22@c:23@n,ca,c 60 sym #99 C6 center :17 axis :24,58@ca newModel true setattr #1.1 chains chain_id A create true setattr #1.2 chains chain_id B create true setattr #1.3 chains chain_id C create true setattr #1.4 chains chain_id D create true setattr #1.5 chains chain_id E create true setattr #1.6 chains chain_id F create true delete #99 rename #1 tmCLIC1 rename #1.1 tmCLIC1-A rename #1.2 tmCLIC1-B rename #1.3 tmCLIC1-C rename #1.4 tmCLIC1-D rename #1.5 tmCLIC1-E rename #1.6 tmCLIC1-F # ---------------- EGFRv3 ---------------- #runscript egfrv3_v1.cxc # ---------------- OSMR ---------------- open Q99650 fromDatabase alphafold version 6 id 3.1 center 0,0,0 torsion #3.1:804@c:805@n,ca,c 60; torsion #3.1:805@n,ca,c:806@n 45 torsion #3.1:805@c:806@n,ca,c -120; torsion #3.1:806@n,ca,c:807@n 130 torsion #3.1:806@c:807@n,ca,c -120; torsion #3.1:807@n,ca,c:808@n 130 torsion #3.1:807@c:808@n,ca,c -120; torsion #3.1:808@n,ca,c:809@n 130 torsion #3.1:808@c:809@n,ca,c -120; torsion #3.1:809@n,ca,c:810@n 130 delete #3.1:836-979 rename #3 OSMR rename #3.1 OSMR-I combine #3.1 modelid 3.2 name OSMR-J setattr #3.1 chains chain_id I create true setattr #3.2 chains chain_id J create true turn x 270 models #3 turn z 180 models #3.1 move y 90 models #3 move x 200 models #3.1 move x -200 models #3.2 # ---------------- DISPLAY ---------------- delete ~protein rainbow #1-3 structures palette Paired-12 surface #1-3 transparency 0.5 move x 5.08443251 models #1 move y -47.21837099 models #1 move z -14.00102839 models #1 #turn x -67.233 models #1 center 0,0,0 #turn y -31.805 models #1 center 0,0,0 #turn z -69.036 models #1 center 0,0,0 define axis #1 primary false tertiary true radius 1 padding 100 id 4.1 define axis frompoint -300,0,0 topoint 300,0,0 color red id 4.2 define axis frompoint 0,-300,0 topoint 0,300,0 color green id 4.3 define axis frompoint 0,0,-300 topoint 0,0,300 color blue id 4.4 view position #1 sameAsModels #4.4 angle #4.1 #4.2 angle #4.1 #4.3 angle #4.1 #4.4

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New ChimeraX Plugin: Cube'n Tube
by Cairoli Tamino 24 Feb '26

24 Feb '26

Hey all, I’m happy to share a small plugin I recently developed for UCSF ChimeraX: Cube’n Tube. It extends the standard eraser sphere tool. Instead of only a sphere, you can now erase with cubes, cylinders (frustum), cones, or even define your own custom shape. While working with various protein structures, I often felt that a spherical eraser is not always ideal. Especially when trying to remove part of a filament, micelle density, or isolate one asymmetric unit of a larger assembly. I was really missing a more dynamic eraser tool, so I decided to build it. I also implemented a simple undo/redo function for the eraser tool. I cannot count how often I misclicked and had to restart my masking from zero… Now there is a one-step undo (limited to one step to keep it smooth on all machines). The custom shape option works particularly well together with a fitted atomic model (for example from AlphaFold) to erase everything outside the region of interest. Cube’n Tube can be downloaded directly from the ChimeraX Tool Shed or from GitHub (https://github.com/TaminoCairoli/CubeNTube) If you are missing a feature or have ideas for improvements, feel free to open an issue on GitHub. Many thanks to the team (especially Tom Goddard) at University of California, San Francisco for building such a powerful and well-documented tool, and thanks to Pavel Afanasyev, Julius Rabl and Dianhong Wang for discussion and testing. Best, Tamino

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Trouble with ISOLDE installation.
by Michel THEPAUT 23 Feb '26

23 Feb '26

Dear help team, I try to install ISOLDE from ChimeraX, using Tool / More Tools... menu: Clicking on Install looks to work, because I have the information below which appears un Log of ChimeraX But it looks like nothing happens as progression bar (red arrow above) do not progress, even after more than half an hour. I am using ChimeraX installed thanks to SBGrid: Is there a known problem or an other way to do this installation ? Thank you for your help. Best regards. -- Michel Thépaut Institut de Biologie Structurale MIT/M&P CAMPUS EPN 71 avenue des Martyrs CS 10090 38044 Grenoble Cedex 9

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Improvements to ChimeraX 1.11.1
by Anindya Karmaker 20 Feb '26

20 Feb '26

Hello, I am a final year grad student at UCD and among many of my passions and recently acquired skills molecular biology/simulation is one of them. I have been using ChimeraX for some time now to learn and have used it extensively as well. But with every changing version I find wide gaps between functions.In the recent version 1.11.1 some commonly used functions like icoshedral have been completely removed and syntax changed. I develop applications for fun and utility as well and I understand that change is necessary. But you also have to understand backward compatibility. You simply cannot remove a function and expect people will adapt to it. Please do not remove syntax and backward compatibility. I understand that you may or may not be using AI to improve the application but one thing I found is that AI will hallucinate and will try to make changes or rewrite unnecessary code to prove its superiority which sometimes just removes backward compatibility. I would really appreciate it if you would understand my frustration. Just my two cents. Thank you. Sincerely, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker(a)ucdavis.edu <akarmaker(a)ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/>

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Helpful cheat sheet for ChimeraX
by Alejandro Daniel Pereira 19 Feb '26

19 Feb '26

Hi ChimeraX team, My name is Alejandro Pereira, and I am a PhD candidate in the Trent Lab with the Department of Microbiology at the University of Georgia. I recently created a ChimeraX cheat sheet that highlights a range of useful features and includes publication‑quality examples. As a developing scientist, effective science communication is extremely important to me. With that in mind, I wanted to ask whether the ChimeraX team might be interested in including this cheat sheet on your documentation page or website. My goal is to provide beginners with a clear, accessible resource that introduces core concepts and showcases key features without the potential confusion of navigating extensive documentation. If this is something you’re interested in, please let me know, and I’d be happy to send it over. I only ask that proper citation be included to ensure appropriate credit. I’d also be glad to adapt the material to meet any formatting or style preferences you may have. Best, Alejandro Pereira Microbiology Department Trent Lab Ph.D. Candidate e: Alejandro.Pereira(a)uga.edu<mailto:Alejandro.pereira@uga.edu> [University of Georgia]

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clip
by Timothy Springer 15 Feb '26

15 Feb '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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