April 2026 - ChimeraX-users - RBVI Mailing Lists

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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Boltz pae contacts
by Nathan Davis 21 Apr '26

21 Apr '26

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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Sequence selection and export tools
by Samuel Haysom 21 Apr '26

21 Apr '26

Hi, Not sure if I'm missing this but there are a few sequence selection and export tools that I can't seem to find an easy way to do: 1. Is there a way to select two locations on a protein chain and then expand the selection to include all the residues between those two points? 2. If a continuous stretch of residues is selected, is there a way to print the sequence to the log or to copy it to the clipboard? 3. In the sequence view, is there a way to select a stretch of residues and then copy that to the clipboard? In general it would be really nice if copy worked in the sequence view window on selected residues I'm aware that I could script this functionality but it does seem to the sort of thing that might be possible in the vanilla installation. KR, Sam Samuel Haysom Senior Scientist • Protein Sciences Nxera Pharma +44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Nxera Pharma UK Limited. Registered Office: Granta Park, Great Abington, Cambridge, Cambridgeshire, CB21 6DG. Company No: 06267989

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Chimera X color question
by Michael Moos 14 Apr '26

14 Apr '26

Hello, I try to color different parts of a molecular chain and am stuck with the problem that I can not define the fill color individually for the selected parts. The color is valid for the selected sticks but fill color changes for the whole molecule. Is there a solution for this problem? It works if I cut the molecule in different parts but I would like to keep it as whole. The program itself is very nice and I prefer to use it for displaying long molecules. A color code would be necessary for marking the different parts of the molecule for better visualization (see attached file). Kind regards, Michael -- Dipl. Chem. Michael Moos Universität Würzburg Institut für Organische Chemie Lehrstuhl für Physikalische Organische Chemie AK Prof. Lambert Am Hubland C1 97074 Würzburg Phone: +49931 31 88764 Fax: +49931 31 88764-0 Web: https://www.chemie.uni-wuerzburg.de/oc/lambert-group/

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