- ChimeraX-users - RBVI Mailing Lists

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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Protein-Protein Interaction Prediction
by Charity Conlin 19 Mar '25

19 Mar '25

Hello, I am trying to use ChimeraX to predict the interaction of 2 proteins using alphafold: Beta-Lactoglobulin and Lactoferrin. I have plugged the 2 protein sequences into the alphafold tool to try to predict the interaction, but I get a failure code in google colab. I am wondering how I can get around this? I think it is because the wrong versions of numpy and colab are installed during the program. Thanks, Charity [cid:b73a7660-3878-48cf-87d5-ddcd6ab388c2]

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Poor performance on Ubuntu w/ discrete graphics vs basic b laptop
by ben 19 Mar '25

19 Mar '25

I'm looking for trouble shooting tips on poor graphics performance on linux. I have read through the FAQ's and done a basic search of the chimera list. Observed: Symptom: Prohibitively slow rendering when just rotating a map, especially if a model is loaded as well. When using Isolde (and presumably anything with clipper) performance is more "normal" as only a small portion of the map is displayed. System: This is observed on Ubuntu distros (both 20.04 22.04) with their respective Chimerax packages, tested versions 1.6.1 and 1.9. Nvidia drivers installed via the cuda toolkit (535.183.01 CUDA Version: 12.2 ) GPUs are either rtx 3090 or 4090s Point of reference: Performance is compared to my relatively very underpowered Windows thinkpad w/o discreet graphics. Thanks for any pointers to resources! Ben Sent with [Proton Mail](https://proton.me/mail/home) secure email.

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Issue with crashing after mac upgrade to Sequoia
by Lee, Juliet A. 19 Mar '25

19 Mar '25

Hello! I recently updated my Mac (M2) to Sequoia 15.3.2, and I have had a specific issue in ChimeraX since then (though I cannot be 100% positive the two things are linked). Basically - whenever I try to save (anything) in ChimeraX, the application stops responding and I have to quit it. I downloaded the newest version 1.9 of ChimeraX as well as the daily build version - but this problem persists. I read about issues with the graphics driver - but these seem to be limited to Intel chips... Hoping you might have some insight as to why this is occurring, thank you!!! Sincerely, Juliet

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secondary structures
by Bajaj, Ruchika 18 Mar '25

18 Mar '25

Hi I want to determine helices and betasheet and their ranges in a structure. Could you please let me know which command and its usage I can use to get it. Please let me know. Thanks !! Regards Ruchika

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Request for Review of Figure 12 instructions
by Zeenat Bashir 18 Mar '25

18 Mar '25

Dear ChimeraX Developers, I hope this email finds you well! I am developing a hands-on module for students using ChimeraX, and I want to express my appreciation for this powerful and beautifully designed tool. I would like to request a review of the instructions on page 11 for generating Figure 12. I have successfully generated this figure before and am now attempting to do so using ChimeraX. However, I would appreciate your guidance to ensure the accuracy and clarity of the instructions (I have highlighted it in red) Thank you for your time and support! I look forward to your feedback. Best Regards, Zeenat -- *Dr. Zeenat Bashir* *Senior Lecturer* *Biotechnology Lab Coordinator* *Department of Chemical and Biomolecular Engineering* *University of Pennsylvania* *310 Towne Building* *220 S. 33rd Street* *Philadelphia, 19104 -6393* bashirz(a)seas.upenn.edu

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sybyl vs amber atom types in ChimeraX
by laurene.jacquot 17 Mar '25

17 Mar '25

Dear ChimeraX community, I hope this message finds you well. I am a master student currently working on a project where I need to generate a mol2 file with amber atom types for a protein. Chimera does not manage to parametrize my protein at all, which is why I switched to ChimeraX. ChimeraX does manage to generate a mol2 file, but it writes sybyl atom types. Despite looking on forums, I have not found a feature like in Chimera to write amber atom types instead. I was wondering if such a feature exists in ChimeraX ? Thanks in advance, Best, Laurène Jacquot PSL University, ChimieParisTech

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Automating the process of data generation via ChimeraX
by mishra.ananya.163＠gmail.com 17 Mar '25

17 Mar '25

Dear Sir/Madam, I am an undergraduate student working on a project and I am trying to generate values for the solvent accessible surface area, mean molecular lipophilicity potential and mean surface electrostatic potential for a dataset involving protein 3D structures (in pdb format). We also plan to introduce point mutations via ChimeraX using the swapaa command and measure the same values for the mutated proteins. As such, we were wondering if there is a way to automate this process of generating the values for each protein, without having to manually do it. We tried to test out some code to see if it is possible to run a python file in ChimeraX. This was the code we wrote: import chimerax import csv import os from chimerax.core.commands import run run(session, "open" + r'C:\Users\anany\Downloads\Research\Test_PDB_Passenger\P35579_MYH9.pdb') run(session, "color red") run("surf") However, we received this error message: openC:\Users\anany\Downloads\Research\Test_PDB_Passenger\P35579_MYH9.pdb Traceback (most recent call last): File "C:\Users\anany\Downloads\Research\Test_PDB_Passenger\test_import.py", line 6, in <module> run(session, "open" + r'C:\Users\anany\Downloads\Research\Test_PDB_Passenger\P35579_MYH9.pdb') File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3156, in run raise UserError(self._error) chimerax.core.errors.UserError: Unknown command: openC:\Users\anany\Downloads\Research\Test_PDB_Passenger\P35579_MYH9.pdb Error opening python file C:\Users\anany\Downloads\Research\Test_PDB_Passenger\test_import.py We would appreciate your kind assistance! Thank you!

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Feature request alphafold: return selection when dragging in PAE plot
by Vorländer,Matthias Kopano 17 Mar '25

17 Mar '25

Dear ChimeraX team, I love the alphafold tools in ChimeraX, and have a small suggestion to make it even better. Currently, when associating a PAE plot from a JSON file, you can drag the mouse in the PAE plot to color the corresponding residues (magenta and lime), but the residues do not become selected (although the color command gets printed in the log). I think it would be helpful if there was an option (or default behavior) to return a selection in addition, so that the selected region could be saved as a named selection, the display style changed ect… Or am I missing anything? Many thanks in advance, Matthias

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