December 2025 - ChimeraX-users - RBVI Mailing Lists

RHEL/Rocky/AlmaLinux/etc 10 releases available
by Greg Couch 03 Dec '25

03 Dec '25

We are pleased to announce that you can now get 1.11 release candidates and daily builds for Red Hat Enterprise Linux 10 and derivatives. For example, Rocky 10 and AlmaLinux 10. A more complete list can be found on wikipedia, https://en.wikipedia.org/wiki/Red_Hat_Enterprise_Linux_derivatives. Since this is a new platform for ChimeraX, it hasn't been tested as thoroughly as the other platforms. We expect the RHEL 10 releases to be bug-for-bug compatible with the RHEL 9 releases, but there is a chance that they aren't. So please try one out and report any bugs you find. -- Greg

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Colouring Amino Acids Within A Selected Region
by Nusrat Tazkia 03 Dec '25

03 Dec '25

Hello ChimeraX developpers, I hope you are doing well. I was trying to colour each amino acid present within a selected region of my model and couldn't figure out how to do it. Could you please guide me on how to do it? I ran these commands (for examples for chains A and E) and have attached my model in this email as well: interfaces select /A contacting /E bothSides true color sel red Please let me know at your earliest convenience. Thank you, Nusrat Tazkia

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How to measure the correlation length of a map in ChimeraX
by 张楠 02 Dec '25

02 Dec '25

Dear ChimeraX Developers, I have an EM density map and need to measure its diameter and height. I used the "measure and color blob" tool, which displays the length, width, and height of the entire EM density when clicked. However, the values are measured around the entire density map, making them slightly larger than the actual diameter. Therefore, I tried using the "tape" tool to measure, but it is difficult to select two perfectly horizontal points for an accurate measurement. I would like to ask how to measure the correlation length of a map in ChimeraX. Looking forward to your answer, thank you! Best regards, Nan Nan Zhang zhangnan(a)nankai.edu.cn

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Alpha-fold-chimerax-coot - incompatibility
by Abhilash Padavannil 01 Dec '25

01 Dec '25

Hi All, I am having trouble with .cif files in Chimerax — I re-built the model (Model-Angelo) in coot using alpha-fold models for completion and saved it as a .cif file. When I open the file in Chimerax certain proteins in the complex show up differently and the their chain IDs are missing in the Chimerax list. Could you help me fix this ? Previously I was able to combine the individual alpha-fold models to a single in Chimerax .cif file. However, if I do local refinement in coot the chains go back to being different. Please suggest. Attached is the screen shot for reference. Thank you. [cid:d13d01b7-12bf-4117-8bbe-f63d6679629a@namprd08.prod.outlook.com]

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GPU/CUDA support for toolshed deep learning plugin
by HAWICKHORST, BRYAN 01 Dec '25

01 Dec '25

Hello, I am a student from Professor Jing He's lab at Old Dominion University. I am trying to enable GPU acceleration for our deep learning plugin, DeepSSETracer. The problem I am running into is that python in the chimerax environment cannot see cuda. Varying cuda versions seems to rule out including cuda as a dependency. Additionally, we would like to avoid custom cuda installations via the chimerax terminal, as it would greatly complicate installation for the users of our plugin. Is there a way to support cuda or GPU acceleration in another way (that ideally does not require user interaction with the chimerax terminal)? Or, could you point me towards tools that have managed to do this? I found this library, ONNX Runtime and wonder if it may be useful: https://onnxruntime.ai/docs/get-started/with-python.html#install-onnx-runti… Best regards, Bryan Hawickhorst Old Dominion University

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