March 2025 - ChimeraX-users - RBVI Mailing Lists

AI in ChimeraX
by Elaine Meng 07 Mar '25

07 Mar '25

On Mar 7, 2025, at 6:01 AM, Veach, Kevin G. <kevin.veach(a)uky.edu> wrote: > > Hi Elaine: > Does Chimera-X use Artificial Intelligence or Large Language Learning Models? > Thank you, > > Kevin > Kevin Veach, Computer Support Specialist II > University of Kentucky, Animal & Food Sciences Dept. Hi Kevin, Please use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address CC'd here for general questions about ChimeraX -- I'm not the top expert on all parts of ChimeraX, so you may get better answers from other developers or our user community. Regarding your question, my understanding is that ChimeraX itself does not use these kinds of calculations, but it has tools that interface to web services or other calculations (run outside of ChimeraX) that do use them. The ones that I can think of are AlphaFold/ColabFold and ESMFold: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html#predict> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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Creating movie in ChimeraX from YASARA simulation
by ibogdanov 07 Mar '25

07 Mar '25

Hi ! I have the following question - How can I create a movie, when I cannot use the YASARA.sce file from which I converted/extracted xtc.file(the trajectories) when I have all the snapshots(pdb and sim.files) created as separate files during the performed simulation in YASARA...I've uploaded for example the first pdb file of the series and the xtc.file but isn't the saved xtc.file(trajectories) of the whole simulation(for all the structures)? How would you suggest me to solve this problem, if ChimeraX doesn't support sce.files ? Thank you in advance! Kind Regards, Ivan Bogdanov

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Problem installing on OSX
by Thom Hughes 06 Mar '25

06 Mar '25

I apologize for the dumb question, but here it is. I want to install the isolde extension. When I go to more tools, isolde, and click the install button a .whl file downloads correctly. But then nothing happens. I’m running OSX 15.3.1. thanks in advance for any pointers!

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Unable to open the file after downloading ChimeraX
by Guo-Ping Zhou 05 Mar '25

05 Mar '25

Dear Sir/Madam, After downloading ChimeraX, I automatically get the attached .png in the application as a microsoft word file. However, I can't open the Quick Access Toolbar. Could you please tell me how to make it work? Thanks! Guo-Ping Zhou, Rocky Mount Life Sciences Institute, Rocky Mount, NC 27804

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(no subject)
by FRANGIE Christian 05 Mar '25

05 Mar '25

Dear UCSF ChimeraX Support Team, My name is Christian frangieh, I am currently using Chimera X to visualize my AlphaFold simulations, and I want to check when i introduce a mutation and change one residue (amino acid), whether there is a change in the surface accessibility of the residue. Currenlty i am checking this visually by checking whether the residue is exposed to the surface or hidden. Nevertheless, i would like to know how can i do this with a command or by some form of calculation or structural analysis. Can you please help me with this matter? Warm Regards, Christian

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Can not find Structure Minimization in ChimeraX menu
by N.B. Nugroho 04 Mar '25

04 Mar '25

Dear ChimeraX developers I a little bit confuse to find the Structure Minimization menu in ChimeraX. In Chimera 1.16 it located in menu Tools>Structure Editing>Minimize Structure. Could you please guide me for this little problem. Best regards Nuki B Nugroho

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(no subject)
by junjie han 02 Mar '25

02 Mar '25

Hi, I hope you are doing well. May I ask two questions? First one: Why does the connection part between the side chain and backbone, which is circled in a dashed line in ChimeraX, look so abnormal? How can I make it display normally? [cid:437c0c59-2e31-4251-ac9c-eff3f64af0dd] Second one: Is it possible to show the border only for a specific region of protein without hiding other regions? Thanks, Junjie

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