- ChimeraX-users - RBVI Mailing Lists

Coloring chains by attribute
by Juan Ortiz Mateu 02 Oct '24

02 Oct '24

Dear developers, I’m trying to color the ribosome (4ug0) with a color code for abundance of each chain (ribosomal proteins) found in my proteomics data. I have created an attribute successfully, as it says in the log: Summary of feedback from opening fc.defattr note Assigned attribute 'FC' to 32 chains using match mode: any However, in the Render/Select by attribute tool there is no option to color chains, only atoms/residues/structures. How can I apply these numeric values to color the different chains/subunits? Thank you, ******************************** Juan Ortiz Mateu Researcher PhD Student Membrane Proteins Lab Biotecmed Institute University of Valencia Dr. Moliner, 50 46100 Burjassot (Valencia) Spain research.uv.es/membrana/ **********************************

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system log of ChimeraX
by Enrico Martinez 02 Oct '24

02 Oct '24

Dear ChimeraX users! I wonder if there is some system log file containing the full history of previously executed commands and scripts in Chimera-X on the linux machine ? This could be useful if I did not save something and would like to resolve the full story. All the best, Enrico

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Pre-fitted structures
by Eric Pettersen 01 Oct '24

01 Oct '24

Hi Randy, I'm attaching a wheel file where the Fit in Map tool (and phenix emplaceLocal command) supports pre-fitted structures. Use the "toolshed install <drag-and-drop wheel file>" command to install it. I guess I could now use an example system where emplace_local returns more than one solution, so I can work on a browsing interface for results. --Eric

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Chimera X opening issues on windows machineGood Afternoon,
by Haroon, Shohaib (NIH/NICHD) [C] 01 Oct '24

01 Oct '24

Good Afternoon, Hope this email finds you well. I am reaching out to your regarding an issue after successfully installed the latest version of Chimera X on one of my user he is using windows desktop and not able to open it. Even though I tried it multiple versions same issue persist. I installed the same version on my laptop without any issues and working fine. Is there anything need to do differently so it can open on desktop. Much appreciated for your help Thank you Shohaib Haroon Desktop Support Technician Information Resources Management Branch Eunice Kennedy Shriver National Institute of Child Health and Human Development 6710B Rockledge Drive, Bethesda, MD 20817 cell:301-275-0276 Email: shohaib.haroon(a)nih.gov<mailto:shohaib.haroon@nih.gov>

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Increasing ChimeraX speed?
by Altobelli, Chad 30 Sep '24

30 Sep '24

Hi, I love using ChimeraX to make morphs, but my protein is quite a large hexamer (500kda) and the progression through the coordset can be quite slow during playback. When I look at my Windows taskmanager, I can see that neither my CPU (12th Gen Intel i7-12700H), RAM, or GPU (NVIDIA RTX 3050 Laptop) are maxed out. Is there a way to speed up Chimera morphs? Thanks, Chad

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Molecular Dynamics in ChimeraX
by Enrico Martinez 30 Sep '24

30 Sep '24

Dear ChimeraX users! I noticed that in ChimeraX there is no built-in molecular dynamics simulation engine as opposed to the older UCSF Chimera. Is it possible to use some visualization trick to deform slightly static coordinates of atomic selection introducing (visually) the impression that they move during movie recording ? Many thanks in advance Enrico

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Software copyright consulting
by 姜恩誉 27 Sep '24

27 Sep '24

Hello, is the application of your Chimera X software for paper publication a non-commercial use？ Looking forward to your reply. Thank you 姜恩誉 2023111025(a)stu.njau.edu.cn

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info distmat command
by NUR AIDA SAKINAH 27 Sep '24

27 Sep '24

Hi ChimeraX teams, Can you guide me to use the *atoms-spec* for info distmat command. I want the output in chimerax log to list out distances between drug compound and the amino acids side chains and only display the distances below than 4 A. For now, what i have got, the output include distances between atoms in the drug itself and atoms in the amino acids itself. The command that i have try are: 1. info distmat (protein & sideonly) | :dex ::num_distance< 4 2. info distmat (protein & sideonly) | :dex 3. info distmat (protein & sideonly) & (:dex) distance < 4 Hope you could help me with this. Regards with thanks, Aida.

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Atoms command spec
by NUR AIDA SAKINAH 27 Sep '24

27 Sep '24

Hi ChimeraX teams, Can you guide me to use the *atoms-spec* for info distmat command. I want the output in the chimerax log to list out distances between *the drug compound and the amino acids side chains and only display the distances below than 4A*. For now, what I have got, the output includes distances between atoms in the drug itself and atoms in the amino acids itself and I don't want that. Only display distances between atoms of the drug and the amino acids side chains. The protein and drug details: PDBID= *4YVP* with drug compound *DEX* The drug binding site distance is below than *4A*. The command that i have try are: 1. info distmat (protein & sideonly) | :dex ::num_distance< 4 2. info distmat (protein & sideonly) | :dex 3. info distmat (protein & sideonly) & (:dex) distance < 4 Hope you could help me with this. Regards with thanks, Aida.

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How to increase the font size of pseudobond labels
by Suhas Srinivasan 26 Sep '24

26 Sep '24

Dear ChimeraX Community, I was trying to increase the default font size of the very small labels displayed on the pseudobonds that are generated from the “distance” command. Selecting the pseudobond label and then using the command “label size 512” had no effect. Your help would be appreciated and thank you for your time. UCSF ChimeraX 1.8 macOS 14.7

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