April 2026 - ChimeraX-users - RBVI Mailing Lists

Error in AlphaFold
by Chang, Ju Fang 01 May '26

01 May '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 24 Apr '26

24 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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ChimeraX download mirror is down
by Elvio Rodriguez Araya 23 Apr '26

23 Apr '26

Hello, I am about to teach a course in structural bioinformatics, and the first step is to download ChimeraX 1.11.1, but the download link is dead. Basically, the course would be suspended if the link doesn't work. Is there any chance for you to share at least the EXE file with me? Sorry for the inconvenience Regards, Elvio -- Dr. Elvio Rodríguez Araya Facultad de Ciencias Bioquímicas y Farmacéuticas, UNR Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET) Suipacha 590, Rosario, Argentina

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Suggestion
by Samo Lešnik 23 Apr '26

23 Apr '26

Dear developers, I have a small suggestion: if the residue name is detected as HOH, TIP3, WAT, ... (whatever the list of waters are), then the bond between H2 and H1 is not drawn, as this is an artifact of the small distance. Best regards, Samo

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New feature request: "shortCircuit" option for clashes command to terminate as soon as single clash is found
by Jon David 23 Apr '26

23 Apr '26

Hi team, I'd like to request new functionality for the clashes command. Specifically, I'd like to request for a new option called "shortCircuit that accepts a Boolean value: True or False. If True, then as soon as any clash is detected, the clashes command terminates; False, then behave the way it does now. For my particular use case, I am making collision checks between pairs of molecule configurations, thousands of pairs. The problem is the more clashes there are, the longer it takes for the clashes command to finish. This is a problem when I'm checking for collisions thousands of times. To have a feature where the clashes command exits early, as soon as it finds ANY clash/collision, would be extremely useful for my case. Thanks, --J

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