October 2024 - ChimeraX-users - RBVI Mailing Lists

Functionality request: Measure molecular weight
by Jan-Hannes Schaefer 04 Oct '24

04 Oct '24

Dear ChimeraX community, Thanks for your work and effort in making ChimeraX available to all of us. I would love to see a function in future versions of ChimeraX to measure the molecular weight of the model and link it to the uniprot entry? Let me know if this is something you would like to add. Yours, Jan ___________________________ Jan-Hannes Schäfer, PhD Lander Group • Scripps Research 10630 John J Hopkins Dr. San Diego, CA 92121 Mailing-code: TRY-21 jschaefer(a)scripps.edu (858) 784-8728

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Selecting a sidechain but not the cartoon backbone
by James Lingford 03 Oct '24

03 Oct '24

Dear ChimeraX team, I want to select only the sidechains of a protein in order to visually outline them for a figure. This isn't an issue if cartoons are turned off, because I can select the only sidechains I want and use the command: `sel sel & sidechain` and I outline them in a nice way with... `graphics sel col black width 2` However, if cartoons are turned on then this won't select just the sidechain, but select a portion of the cartoon backbone too. I'm not sure how to specify this. Ideally I want a transparent cartoon with opaque sidechains, and then have only the sidechains selected. Please see the images attached for examples of what I'm referring to. Many thanks, James [image: sidechain2.png] [image: sidechain1.png] -- *James Lingford* | Research Officer, Greening Lab Department of Microbiology, Monash Biomedicine Discovery Institute Monash University Google Scholar <https://scholar.google.com/citations?user=4KSRHTUAAAAJ&hl=en> | Website <https://www.jameslingford.com/>

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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 02 Oct '24

02 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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