April 2026 - ChimeraX-users - RBVI Mailing Lists

MCP for ChimeraX
by Alexis Rohou 20 Oct '26

20 Oct '26

Hi all, I would like to use ChimeraX via an agent. Quick googling suggests I'm not the first person to think of this (here <https://github.com/chatmol/molecule-mcp>, here <https://github.com/GDAmitha/chimerax-alphafold-mcp>), but before I dive in I thought I'd check - anyone else actively working on this? Or maybe you have worked on it and hit a roadblock? Cheers, Alexis

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clip
by Timothy Springer 10 Aug '26

10 Aug '26

Can you translate this into a clip command I can use in a .cxc file? clip list Using 2 clip planes: near offset -3.0783, axis -0.462,-0.880,0.109, point on plane 218.1,184.5,202.4) far offset 12.676, axis 0.462,0.880,-0.109, point on plane 210.8,170.6,204.1) - Tim *Timothy A. Springer, Ph.D.* Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

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cartoon style setting
by junjie han 07 Aug '26

07 Aug '26

Hi, May I ask how I can set the cartoon thick for a specific region of a structure in ChimeraX? For instance, the command "cartoon style #1/A:10-20 thick" plays an effect on the whole #1 molecule, not only affecting the specific region #1/A:10-20. Please let me know what the appropriate command is by any chance. Thanks, Junjie

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Error in AlphaFold
by Chang, Ju Fang 30 Apr '26

30 Apr '26

Hi, There, I think there might be a version compatibility issue, could you please help? Thank you Jufang ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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masking partial xplor volumes in ChimeraX
by Jan Hofmann 30 Apr '26

30 Apr '26

Hello, I am overlaying electron densities from xplor files with .pdb structures. The problem is that the .xplor files only crop along X, Y and Z with the vop cover # fbox command. Is there any command or option to hide some of the xplor densities, but not all? I have a screenshot attached and would like to hide the density volume circled. If not, can xplor files be converted into a different file type that allows that? Thank you. Best, *Jan Hofmann, M.Sc.* *PhD Candidate, Department of Chemistry* *Chapman Group* Stony Brook University *jan.hofmann(a)stonybrook.edu <andrew.nicoll(a)stonybrook.edu>* Office: Room 577, Chemistry [image: image.png]

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Opening mol2 files with ChimeraX without ViewDock windows
by Ute Roehrig 30 Apr '26

30 Apr '26

Dear Developers, Is it possible to change the default behavior of ChimeraX when opening files in mol2 format to not showing the ViewDock window? I know I can add "showtool false" on the command line or make an alias, but I often open multiple mol2 files directly from the linux command line (chimerax *.mol2), and then the screen becomes cluttered with ViewDock windows. Alternatively, is there a command to close all opened ViewDock windows? Thank you for your help, Ute

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collapse atom-atom pbonds into residue-residue contacts
by Weiskopf, Erika Nicole 28 Apr '26

28 Apr '26

Hello, I want to visualize atom-atom pbonds (generated through the contacts feature) as single residue-residue contacts. Is there a way to do this and/or a way to delete single pbonds I have selected to manually clean up the image? Thanks, Erika The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Question about openfold command line syntax
by David S. Fay 27 Apr '26

27 Apr '26

Hi, I couldn’t find documentation regarding the correct syntax for running multiple models and using different seeds from the ChimeraX openfold platform. I tried something similar to what has worked for boltz: openfold predict #1/A #1/B recycle 3 seed 3 samples 5, but got an error (Expected a keyword). Tried a few other iterations but came up empty. Thanks in advance. David Fay

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Angle between an axis and a plane
by Alexandra Zahradnikova 24 Apr '26

24 Apr '26

Dear All, I am trying to calculate a set of angles between pairs of axes and planes. Example: sel #1/B:348,1052 @ca; define axis sel; sel #1:1052 @ca; define plane sel; angle #1.3 #1.4 My problem is that the angle is always reported positive, no matter whether the axis goes "up" or "down" from the plane, when "up" and "down" are defined relative to the orientation of the molecule. Is there any way how to distinguish between these two cases automatically? Thanks very much in advance. Best regards Sasha Zahradnikova

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Protein-protein interactions assessed through Boltz using ChimeraX consistently scoring quite low
by David S. Fay 23 Apr '26

23 Apr '26

Greetings, We’ve been working with largish data sets and testing for protein-protein interactions using AF2, AF3 and Boltz. For many of these tests we’ve run the prediction programs locally on our supercomputer. We’ve also done a good amount of primary testing and double-checking using web-based interfaces available for CoLab(AF2) and AF3. I just recently started using Boltz2 through the ChimeraX interface. What I’ve noticed so far is a pattern where the Boltz prediction through ChimeraX is giving much lower interaction scores, based on ipTM and PAEs, than Boltz through our supercomputer as well as AF2 and AF3 through our super computer or via the web. I’ve tried running multiple models, seeds, and increasing recycles to 3 as well as checking the two different boxes (Use steering potential vs. Use MSA cache). The commands I’ve run might look like: boltz predict #1/A #1/B recycle 3 seed 4 samples 5. In any case, I’m puzzled as to why the scores are consistently lower. I recognize that I may be doing something wrong. For example, I seem to need to start out by running a first round of Boltz using the interaction window. Then once I get the first prediction, I can next invoke the “boltz predict” as above using different parameters on the command line. (These parameters are not part of the menus in the Boltz window that I can find.) The different runs, seeds, and models, I’m getting do give slightly different results, but they all seem to be under predicting what we know to be are quite strong interactions. I should say that we also see some differences between local and web-based AF3 and AF2 results, but they aren’t as extreme as what we’re seeing from Boltz from what we can tell. Any thoughts? Thanks greatly in advance! David David S. Fay Ph.D. Professor, Department of Molecular Biology Director (PD/PI), National Institutes of Health Wyoming INBRE University of Wyoming email: davidfay(a)uwyo.edu

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