- ChimeraX-users - RBVI Mailing Lists

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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Ribbon diagram depiction
by Das, Abhinaba 22 Apr '26

22 Apr '26

Hi all, Is it possible to thread a ribbon along non-canonical peptide backbone based helical structure? I was working with CCDC-633286, left is what depicted in the journal article and right is the default view in ChimeraX Thanks, Abhi [cid:3c356f41-2360-426f-86b1-cd758aeca1b0][cid:ae8b49a1-cf5c-4262-9120-dcbb984645b3]

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ChimeraX 1.11.1 compatibility with MacBook Neo (A18 Pro)?
by Ronald Hamilton 22 Apr '26

22 Apr '26

Hi ChimeraX team, I'm considering running ChimeraX 1.11.1 on the new MacBook Neo (A18 Pro, 2026). I noticed the Apple Silicon build is listed as M-series only, so I assume the universal build would be the right one to use. Has the team had a chance to test ChimeraX on the MacBook Neo? Are there any known issues I should be aware of? Thanks for your time and for the continued development of ChimeraX! Best regards, Ronald Sent from Outlook<http://aka.ms/weboutlook>

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Re: ChimeraX locks up in a Mac
by Tom Goddard 22 Apr '26

22 Apr '26

Hi Joseph, This ChimeraX error on Mac is caused by a bug in the Qt window toolkit which appeared with macOS 26. The current ChimeraX daily build uses a newer Qt version (6.10) which appears to fix the problem. The daily build is quite stable, so you may want to use it. It is on the ChimeraX download page. Thanks for the info about Report Bug not working once you hit this error. It must work for some people because this ChimeraX error has been reported dozens of times. Tom > On Apr 21, 2026, at 8:15 PM, Beckman, Joseph S <joe.beckman(a)oregonstate.edu> wrote: > > I wanted to report a reoccurring problem I have been having for the past two months. > > While the program is sitting open and unused, this message popped up and I have to close the program from the kill panel (opt-Escape) > > > > > > I have tried to use Report Bug, but the pop up window does not allow me to edit anything. The machine and software ID show in the window are correct. > > Thanks for all the support you provide, I learn a lot from the posts but am just an amateur. > > >

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how to hide all for a specified spec
by Daniel David Richman 22 Apr '26

22 Apr '26

Hi users, Often when I open a PDB, some residues are shown in both cartoon and atomic display. Often I want to hide both displays, and I can’t figure out how to do this. For instance open 7ubj hide #1 // hides only the atoms hide #1 all // gives an error hide #1 cartoons // this seems to be the only way to hide the cartoons? same story with, for instance hide #1/A Am I missing something? I’m running 1.11.1 on Mac. Thanks, Daniel

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Re: Boltz pae contacts
by Tom Goddard 22 Apr '26

22 Apr '26

Hi Nathan, The error message "No alphafold specified for alphafold contacts" is goofed up -- it should say "No atoms specified for alphafold contacts". This means your structure has no chain A, so your command "alphafold contacts /A to /B distance 5 maxpae 6" needs to be modified to use the actual chain identifiers in your structure. You can hover the mouse over the chains in your structure and it will popup some text indicating the chain id under the mouse. Yes the "Alphafold Error Plot" in ChimeraX works for Boltz 1 and 2, AlphaFold 2 and 3, OpenFold 3, and ESMFold predictions. I plan to rename it Predicted Aligned Error Plot so it will be clearer that it is not specific to AlphaFold. It currently has the AlphaFold name because when I added AlphaFold 2 support about 4 years ago there were no other prediction programs writing PAE. I have fixed the text of the error message in the daily build. Thanks for reporting the problem. Tom > On Apr 21, 2026, at 4:41 PM, Nathan Davis <ndavis18(a)uwyo.edu> wrote: > > I get the error: No alphafold specified for alphafold contacts. I attached my chimerax session. Should I be using alphafold error plot for the pae? > > On Apr 21, 2026, at 11:06 AM, Nathan Davis via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: > > Hi, I'm Nathan. I have been using ChimeraX to assess protein-protein interfaces. One of the commands I use is alphafold contacts, usually with something like this: alphafold contacts /A to /B distance 5 maxpae 6. I started looking at boltz runs as well and realized that this command does not work for boltz models. Is there a similar command that would work for boltz? Also, I'm importing boltz models that I ran on my local cluster. > > Thank you! > Nathan

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