- ChimeraX-users - RBVI Mailing Lists

Ligand flying movie in chimeraX
by Matzov Donna 26 Mar '25

26 Mar '25

Hello, I'm trying to create a movie in Chimerax similar to the "Ligand flying into unbound conformation" that was in the old Chimera movie tutorials (https://www.cgl.ucsf.edu/chimera/data/tutorials/movies08/moviemaking.html) I tried using the "reset" command, but it seems like it doesn't exist in ChimeraX. Is there a command that replaces it? Alternatively, I would be happy for any suggestion for how to get an effect similar to the flying ligand in ChimeraX. Thanks, Donna Donna Matzov, PhD Department of Structural Biology Weizmann Institute of Science The Shalev-Benami Lab<https://www.weizmann.ac.il/Structural_Biology/Shalev-Benami/home>

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Change location of .cache/ChimeraX ?
by James Vincent 24 Mar '25

24 Mar '25

Hello ChimeraX Devs/Users, Is there a way to specify the location of the .cache/ChimeraX directory? As far as I can tell it is always $HOME/.cache/ChimeraX (on Linux machines). I see no options or configs to change this. We are installing ChimeraX on a multiuser system and would like to add a plugin/ bundle to be available for all users ( ChimeraX_ScipionExtensions 1.3). Perhaps I missed this in the documentation, but is there a standard way to add plugins so that they are available for all users? Thanks, Jim

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Force display of helix with setattr
by Kevin M Jude 24 Mar '25

24 Mar '25

For some reason the selected residues in this image are not displayed as a helix in ChimeraX. I think the command to force it woud be ‘setattr sel res ss_type 1’, but nothing changes (the log says “Assigning ss_type attribute to 2 items”). Same result if I try ‘setattr sel res is_helix 1’. Can anybody please set me straight (and my cartoons helical)? Using ChimeraX 1.9 for OS X. Thanks for any help. [cid:image001.png@01DB9CD2.E2CD6B60] -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305

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Inactivate models
by Burgers, Peter 24 Mar '25

24 Mar '25

Dear team, Classic Chimera had a command to turn off specific models, allowing manipulation of the other model(s). What is the command for that in ChimeraX? ChatGPT gave as answer “model toggle off #1” but that appears to be wrong. Thank you, Peter ---------------------------------- Peter M.J. Burgers Marvin Brennecke Professor of Biological Chemistry Department of Biochemistry and Molecular Biophysics Washington University School of Medicine BOX 8231 660 South Euclid Saint Louis, MO 63110 E-Mail: burgers(a)wustl.edu<applewebdata://1B940EF6-0122-4328-902B-DCB358A99492/burgers@biochem.wustl.edu> PH (314) 362-3872 (office) 286-2554 (lab) FAX (314) 362-7183 http://biochem.wustl.edu/~burgersw3/ ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Problem with setting up Modeller
by Miloslav Radoslavov 24 Mar '25

24 Mar '25

Greetings, I encountered an issue when attempting to utilize the "Model Loops" option. After installing Modeller and specifying the path to it, Chimera X did not prompt me to input my activation key. Instead, it indicated that no Modeller key was provided. Also the console command "modeller licenseKey ...." does not seem to work. Could someone please assist me in resolving this issue? Is there an alternative method to input my key? Thank you in advance, M. Radoslavov

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Error using matchmaker
by javisanchezdelrio＠gmail.com 23 Mar '25

23 Mar '25

Hello, I am trying to use matchmaker command (matchmaker #1 to #2 showAlignment true) with two cif files I've obtained from Kihara and Modelangelo. The problem is that, once I try to use the matchmaker command, I obtain the following error: "No matrix compatible with both reference structure and all match structures" and I don't know what is failing. Is it because the two structures are too different from each other? I hope I can get more information about this error message Thank you in advance, Javier

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ChimeraX 1.9 dark theme
by jinlun_kylian zhang 22 Mar '25

22 Mar '25

Hi chimeraX developers, I've used chimeraX for a long time and today I upgraded it to 1.9, But i can't help to notice the chimeraX's theme has been set to dark rather light/white theme in 1.8. Can you please assist me to modify this dark theme back to white? I am more used to that. [image: image.png] Best, kylian

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Switch Dark theme of chimeraX1.9 back to white theme
by hytxnt123＠gmail.com 22 Mar '25

22 Mar '25

Hi, I just upgrade my chimeraX to v1.9 but I dont really fit in the dark theme. Can anyone help me to switch back to the white theme just like v1.8?

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Advice on Meeting settings
by Edwin Kyi 20 Mar '25

20 Mar '25

Hello, We have been experimenting with the Meeting command in VR and are seeing some real uses for guided teaching sessions. We're looking for ways to finesse set up for these sessions and I wonder if you could help with some technical questions we have: 1. What main optimisations of the settings would you recommend for smoother running in VR? 2. Is there an easy way to toggle off all people's interactions with the model with one command except the host? 3. Same as Q2, is there an easier way to toggle off people's hands unless they are the ones asking a question? 4. Can the VR ava VR be resized ie. smaller? Kind regards Edd Edwin Kyi Multimedia Learning Experiences Developer (CTL) Join the VR Society, see: https://www.guildofstudents.com/organisation/ubvr/ +44 121 415 9049 University of Birmingham Collaborative Teaching Laboratory (CTL) Edgbaston Birmingham B15 2TT www.birmingham.ac.uk<http://www.birmingham.ac.uk/> Twitter<https://twitter.com/unibirmingham> / Instagram<https://www.instagram.com/unibirmingham/> / Facebook<https://www.facebook.com/unibirmingham> / LinkedIn<https://www.linkedin.com/school/university-of-birmingham/> [University of Birmingham logo.]<https://www.birmingham.ac.uk/index.aspx> For the most up-to-date-information, visit: www.birmingham.ac.uk<http://www.birmingham.ac.uk/>

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ChimeraX not communicating with GPU
by #TAN YONG JUN EDDIE# 20 Mar '25

20 Mar '25

Dear Developers, Hope this email finds you well. I have encounter an issue regarding the GPU driver usage for chimeraX. The issue is that the model and density movement is very choppy at step size 1, with a box size of 400. Here are some information on the software that I am using. Downloaded Software: Ubuntu 22.04 (Linux) ucsf-chimerax_1.9ubuntu22.04_amd64.deb<https://www.cgl.ucsf.edu/chimerax/cgi-bin/secure/chimerax-get.py?file=1.9/u…> This is my current nvidia driver and cuda version: NVIDIA-SMI 560.35.05 Driver Version: 560.35.05 CUDA Version: 12.6 It came to my attention that it is not utilising GPU upon running "graphics driver" on chimeraX, which outputs: graphics driver OpenGL version: 4.5 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.3 OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits) OpenGL vendor: Mesa additionally, it is not showing up under nvidia-smi when I am running the program. Is there any solutions to this issue? Thank you in advance. Regards, Eddie

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