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December 2025

37 participants
32 discussions

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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