March 2026 - ChimeraX-users - RBVI Mailing Lists

ChimeraX Help: Selective residue labeling for peptide/Protein interface !
by Arun Gupta 09 Mar '26

09 Mar '26

Dear ChimeraX Team, I am currently working on visualizing peptide/Protein complexes and I’m having some trouble maintaining specific residue labels while clearing others. My Goal: I want to label: 1. Protein (Chain A) residues that are within 5.0Å of the Peptide (Chain C) residue 1. 2. The Peptide (Chain C) P1 residue itself. 3. I want to ensure residues P2–P9 remain unlabeled. Below is the script I am currently using: set bg white graphics silhouettes t lighting depthCue f size #1 ballScale 0.20 stickRadius 0.2 select /A & (/C:1 :<5.0) show sel style sel ball color byhet view sel label sel text "{0.label_one_letter_code}{0.number}" label @@display residues bgColor white label height 1.0 sel #1/C: 2-9 label delete The issue I am encountering is that when I execute: sel #1/C: 2-9 label delete it deletes not only the labels for peptide residues P2–P9, but also the labels for the protein interface residues that were previously defined and labeled. Question: * Should I be using a more specific selector in the label command itself to avoid using select and label delete sequentially? Any advice on the cleanest syntax to achieve this would be greatly appreciated! Best regards, Arun Arun Gupta PhD, MRSC Sr. Post Doctoral Research Assistant Gillespie/McMichael Group Nuffield Dept. of Clinical Medicine, University of Oxford, Centre for Immuno-Oncology Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ Tel: + 44 (0)1865 2612913

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Question about changes in alphafold contacts command
by Rowan Cain 09 Mar '26

09 Mar '26

Hello, I am an undergraduate doing research involving protein protein interactions in C. elegans, and I have recently been having some issues with the alphafold contacts command when measuring buried area in protein-protein interfaces. I am running the same batch of dimers that was measured a few years ago with AF2 data, and now with current AF3 data I am seeing vastly different results with the same maxPae, distance values. The main change I noticed with ChimeraX is that the argument in the alphafold contacts command has been changed from “toResidues” to “toAtoms” - is there any reason why this change took place, and would it cause the amount of interacting residues to be measured differently? Thank you, Rowan Cain

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What is the best way to visualize the impact of mutations on the interaction between two proteins?
by jar636＠pitt.edu 06 Mar '26

06 Mar '26

I am working on a project regarding evolution and want to be able to make the necessary mutations on the proteins and then be able to visually see the impact the mutation has on the interaction of the proteins. Specifically, I want to be able to use this information to create a hypothesis as to why these proteins evolved based on the change in interaction. I have tried measuring the distance between the two proteins, but I was wondering what would be the best way to see the biological relevance and overall structural impact of the mutations? Thanks!

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Isolde on ChimeraX 1.11.1 download issue
by Vorländer,Matthias Kopano 06 Mar '26

06 Mar '26

Hi guys, I am trying to install ISOLDE on ChimeraX version 1.11.1 (2026-01-23) for MacOS, but the toolshed says there is no download available for this version. If I however check the Isolde release history, I find version 1.11 <https://cxtoolshed.rbvi.ucsf.edu/download/chimeraxisolde/1.11/1357> from 9 days ago that explicitly states compatibility with ChimerX 1.11.1 on MacOS. Am I missing something or is there some bug? Thanks a lot for your help, Matthias

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What is the ChimeraX color gamut for hex codes?
by Andrew Kennard 06 Mar '26

06 Mar '26

When I color models using hex codes of colors I would like, they are noticeably brighter than the colors I am trying to specify with RGB hex codes. I am selecting colors based on the rest of my figure (which is being built in the sRGB colorspace/color gamut in Adobe Illustrator). I realize that the lighting settings in ChimeraX can change apparent colors, so I am using the "Flat" rendering mode to hopefully minimize that effect. But when I take a hex code I have selected in Illustrator and try to color the model with that hex code, the result is generally brighter than the color I specified. I suspect this is a mismatch in color gamut, but maybe it is still due to lighting? Is there a way to modulate the lighting in such a way that I can try to recover the colors I intend? Thanks! Andrew

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what information goes out from Boltz calculations
by Elaine Meng 05 Mar '26

05 Mar '26

Hi Kirk, Changing subject line and sending to the recommended address for ChimeraX questions chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (just don't include anything proprietary when using it, since it has a public archive), as I'm not the expert on this topic. Others may be able to answer your question more definitively. However, if I had to guess I would say it doesn't send ligand info anywhere because Boltz runs on your local machine, not on Colab, as per the documentation: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/boltz.html> 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 > On Mar 4, 2026, at 3:22 PM, Kirk Nelson <knelson(a)tyra.bio> wrote: > > Hello Elaine, > > It is super cool that Boltz was added to ChimeraX. > > Can you please confirm whether any ligand information is queried against the external database (api.colabfold.com)? > > Thank you, > Kirk Nelson > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: Thursday, December 18, 2025 at 12:35 PM > To: chimerax-announce(a)cgl.ucsf.edu <chimerax-announce(a)cgl.ucsf.edu> > Subject: [chimerax-announce] UCSF ChimeraX 1.11 release > > =-=-=-=-=-=-= > UCSF ChimeraX version 1.11 has been released! > > This will be the last release to support Red Hat Enterprise Linux 8 and > its derivatives. > > ChimeraX includes user documentation and is free for noncommercial use. > Download for Windows, Linux, and MacOS from: > https://www.rbvi.ucsf.edu/chimerax/download.html > > Updates since version 1.10.1 (July 2024) include: > > - 2D Labels and Arrows GUI > - Boltz 2 structure prediction of proteins, nucleic acids, and > small-molecule ligands, with affinity prediction > - Boltz 2 batch ligand-binding predictions (many ligands to same receptor) > - General minimization (including ligands) with Minimize Structure tool > and "minimize" command > - new ViewDock interface (replacing previous ViewDockX) > - new types of trajectory plots: H-bonds, RMSD > - save trajectory plots to image file > - Thermal Ellipsoids GUI > - "chirality" command to report stereocenter chirality > - save/restore scenes including atomic, ribbon, and volume styles and > coloring; more to be added later > > For details, please see the ChimeraX change log: > https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog > > Enjoy! > On behalf of the team, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco

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VR on ubuntu workstation
by arangarajan＠initialtx.com 04 Mar '26

04 Mar '26

Hi, i got steam VR installed but later found out that Oculus does not support linux. Is there a work around for using chimerax VR on latest ubuntu machine with oculus rift s headset? i can get other headset also if it will fit this purpose. thanks in advance, best amith

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RSA Values on Per Residue Basis
by Haley Breckenridge 04 Mar '26

04 Mar '26

Good morning, Is there a way for ChimeraX to calculate RSA values on a per residue basis for an entire structure? I've found software online that can do it by chain, but my structure is made of multiple overlapping chains that would impact RSA values. I understand there is the Interface function in ChimeraX, but I cannot find a way for it to tell me RSA values for each residue in a structure. Thanks! Haley Breckenridge *Haley Breckenridge* PhD Student Molecular Virology Case Western Reserve University

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Import attribute?
by Alexandra Zahradnikova 02 Mar '26

02 Mar '26

Hi All, is it possible to import residue attributes from a text/csv file? For instance, I have some data calculated at an external server, and the output is per residue in CSV format. I would like to view it as color-coded molecule, using the command "render by attribute". Is it possible? Or if not, do you know some workaround? Also, I have these data in a pymol file but I don't use pymol. Is there any way how to read a pymol (CSE) file into chimeraX? Best Sasha ________________________ Alexandra Zahradnikova Institute of Experimental Endocrinology Biomedical Research Center Slovak Academy of Sciences Bratislava Slovakia

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ISOLDE and secondary structure restraints
by Guido Hansen 02 Mar '26

02 Mar '26

Hi all, I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess: Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script? Cheers, Guido -- PD Dr. Guido Hansen Group Leader UNIVERSITÄT ZU LÜBECK INSTITUT FÜR BIOCHEMIE Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen(a)biochem.uni-luebeck.de www.biochem.uni-luebeck.de [1] Ratzeburger Allee 160 23562 Lübeck Links: ------ [1] http://www.biochem.uni-luebeck.de

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