October 2026 - ChimeraX-users - RBVI Mailing Lists

UI suggestion
by Roch, Filip A 23 Oct '26

23 Oct '26

Dear ChimeraX team, I have a suggestion regarding the Tools side panel. Many users that I know struggle with the lack of vertical space in the side panel. I think a feasible fix would be to give users an option to have the side panel extend all the way to the top, with the top tool panel ending earlier (like in the mockup pic 2 vs pic 1). Chimera can already “trim” the top panel if the window is too small (pic 3), so I think it might be possible to implement my suggestion. You could increase the vertical space even more if you'd allow the bottom two bars (command line and the line that shows chain information) to also end where the side panel starts (also pic 2). Please let me know if I can help in any way. Many thanks, Filip Roch Imperial College London [image.png][file-26198a563e09e770990c3b3d083fc949 copy.png] [image.png]

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Running Boltz
by Alexandra Zahradnikova 21 Oct '26

21 Oct '26

Dear All, I tried to install Boltz and the installation was completed without errors. When trying to run Boltz, I got an error message that it was not able to use the GPU. After reinstalling the NVIDIA driver, Boltz recognized the gpu, but I got an error again. I then uninstalled Boltz and installed it again – see the attached installation log. However, it again crashed as shown in the zipped log. My gpu card is NVIDIA GeForce RTX 5070 Ti. I would greatly appreciate your help. Best regards Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796

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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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Legacy Chimera model controls in ChimeraX (chimerax-trimmings)
by Oliver Clarke 19 Oct '26

19 Oct '26

Hi all, Added something to chimerax-trimmings that I have wanted for ages! Added legacy Chimera-style model controls, so that one can freeze or activate specific models and freely rotate/translate them with respect to one another, without having to perform rotation & translation using separate mouse modes, & without selecting the models to be frozen/activated for motion. Implemented as modelmotion in latest version: https://github.com/olibclarke/chimerax-trimmings If there is sufficient interest I will try to migrate this to a bundle so it can be installed/updated from the Toolshed. Cheers Oli

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Re: ChimeraX "camera sbs" on a desktop that takes one side-by-side picture
by Daniel Ramos 14 Oct '26

14 Oct '26

Apologies to the list: my last two messages in this thread were meant as a private reply to Tom, and I sent them here by mistake. Daniel

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Re: ChimeraX "camera sbs" on a desktop that takes one side-by-side picture
by Daniel Ramos 12 Oct '26

12 Oct '26

PS, Tom: places near you to show molecules in stereo to a room. - The field meets almost next door: Stereoscopic Displays and Applications runs every year within IS&T's Electronic Imaging symposium, held in recent years in Burlingame, by San Francisco airport. The other venues, conferences and festivals are gathered here: https://github.com/danielcamposramos/awesome-stereoscopy#conferences-and-fe… - The nearest CAVE I found on record is UC Santa Cruz's CAVE Lab (three walls and the floor, opened in 2015); I could not confirm it still runs. UC Davis's KeckCAVES, where Vrui began, has moved to headsets. - For a group, any modern 3D cinema room can host a presentation through an HDMI 3D-capable projector, and your university may already own one: the projector syncs the glasses, and our desktop feeds it from an ordinary computer. Daniel

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Re: ChimeraX "camera sbs" on a desktop that takes one side-by-side picture
by Daniel Ramos 12 Oct '26

12 Oct '26

Hi Tom, Thank you for this, it is the most useful answer we have had. What you describe from the SGI days is exactly what we are rebuilding: stereo in a window, not full screen, at full resolution, with 2D and 3D on the same desktop, and light glasses. And you named why it disappeared: access. The emitters, the synced graphics cards and the quad-buffer drivers stopped being something people could get, so people stopped even considering stereo. Our approach brings that setup back with what people already own: - The 3D TVs and projectors sold from 2010 on carry the sync themselves: the TV syncs active glasses, and passive TVs use light polarized glasses that keep full colour and serve a whole room. No emitter, no special card. - Any GPU with HDMI: our kernel patches give AMD and NVIDIA's open modules the HDMI 3D modes (Intel has had them since 2013), and frame packing sends each eye at full resolution. - Quad buffer comes back in the desktop instead of the card: our Mesa hands the compositor both eyes, and the compositor makes the picture right for each screen, the way an SR weaver does for its own panel, but for every kind of 3D screen and every program. - On speed: on AMD and Intel, Mesa is the vendors' own OpenGL driver (radeonsi, iris), so this path runs at their normal speed. NVIDIA is where we still have work to do. Anaglyph is only the floor, for someone with nothing else; I agree it is no tool for colour work. Between anaglyph and a 3D TV there is one more cheap step, planned and not built yet: any Android phone in a Cardboard-style viewer, which costs a few dollars, shown by the desktop as one more 3D screen, in full colour. We also work with the DisplayXR developers, whose open OpenXR runtime runs on Linux and Android: our KWin already publishes the window geometry their runtime needs, and we proposed a Cardboard plug-in to them, so OpenXR programs like ChimeraX with `xr on` could reach the same phone. You are right about platforms too: every fix is public, in forks of each project, and offered to it where the project accepts our work, so it can reach other Linux desktops over time. Windows and Mac are beyond our reach. If you would like to try it on any 3D TV or projector when our first image is out, it would be an honour to have someone with your thirty years of stereo as a tester. Thank you, Daniel

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Re: ChimeraX "camera sbs" on a desktop that takes one side-by-side picture
by Daniel Ramos 12 Oct '26

12 Oct '26

Hi Tom, Thank you, and thank you for Greg's notes: they describe exactly the problems our desktop is built to remove. Your page and Greg's notes show the pattern every project we write to has met. Each display brings its own setup: a runtime picked in a vendor's app, a list of known model names, a guess about which eye comes first. The program carries that work one device at a time, and that maintenance is why stereo modes so often fall behind. Our desktop moves that work out of the program: ChimeraX speaks one thing, stereo quad buffers, and the compositor does the per-display part, the same for every program. How it works on Sparky Stereo OS: - ChimeraX runs in sequential stereo (`--stereo`, or `camera stereo`), the mode made for shutter glasses, and asks OpenGL for quad buffers as it already does. - Our Mesa gives it a stereo window and hands the compositor both eyes as one full side-by-side picture, declared as stereo. - Our KWin shows that window in 3D where it is, at full resolution for each eye, while the rest of the desktop (panels, other windows, the pointer) is drawn the same in both eyes and stays flat at the screen. - The compositor converts the result for each screen: HDMI 1.4a 3D for a 3D TV or projector (frame packing, side by side, top and bottom), or red-cyan anaglyph on any monitor. What that changes in Greg's list: - No full-screen mode is needed: the 3D view stays inside the normal ChimeraX window, with its tools and panels around it, flat at the screen, as OpenSCAD's editor did in our stereo build. - The pointer is drawn in both eyes, and ChimeraX gets ordinary mouse coordinates over its whole window, so hovering, selecting and rotating should work as in mono; that is the first thing we will test. The half-window cursor comes from `camera sbs` splitting the window, which this path does not do. - A projector still serves many viewers at once. For the eye-tracked panels, your `xr on` path is the one we would follow on Linux. We work with the DisplayXR developers (an open OpenXR runtime for 3D displays, shipping on Linux): our KWin publishes the window geometry their runtime needs on KDE Plasma. And the vrto3d driver that Andre Michaelis used for the Samsung panels is part of our SteamVR work on Linux, toward 3D TVs. What we offer, respecting our development agenda: - tests of `--stereo` and `xr on` on our desktop, on a 3D TV and in anaglyph, with both eyes captured, reported here; - patches in your style if ChimeraX itself needs any change. And if Greg or anyone here would like to try it when our first image is out, we would be glad to have you as testers: https://github.com/Sparky-OS/sparky-stereo-os/issues/26 Daniel Ramos https://github.com/Sparky-OS/sparky-stereo-os This message was written with AI assistance for clarity.

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ChimeraX "camera sbs" on a desktop that takes one side-by-side picture
by Daniel Ramos 12 Oct '26

12 Oct '26

Hello, I am Daniel Ramos, from Brasília. I make Sparky Stereo OS, a free stereo 3D edition of SparkyLinux (Debian, KDE). Our KWin takes one full side-by-side picture and each screen converts it. ChimeraX already has `camera sbs`, and sequential stereo with `camera stereo` and the `--stereo` startup option. Our Mesa turns OpenGL quad-buffered stereo into that full side-by-side picture, so `--stereo` may work there unchanged. Has anyone used either one on an HDMI 3D display, or in anaglyph on an ordinary monitor? I would like to test it and send the ChimeraX team what I find. Repo: https://github.com/Sparky-OS/sparky-stereo-os In development. Thank you for ChimeraX. Daniel Ramos Written with AI assistance, which I directed and checked.

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Mouse wheel scroll not registered after two-finger drag on Mac touchpad
by Binovsky, Jan 07 Oct '26

07 Oct '26

Dear ChimeraX team, I am experiencing the bug described below on Mac (Tahoe 26.6.) with ChimeraX version 1.12 (2026-06-12). When I open ChX, the wheel scroll works (bound to zoom function). Then, I perform a two-finger action on a touchpad and the wheel scroll is not registered in ChX anymore. Any recommendation on how to mitigate the loss of wheel function other than not to use the trackpad when ChX is open? Best, Jan ######################## Tom Goddard wrote: > Hi Dale, > > I'm guessing your on a Mac and this has something to do with ChimeraX Mac multitouch trackpad support. There was a limitation in the Qt window toolkit where two finger drag on the touchpad produced scroll events even though ChimeraX was handling the two-finger drag to do a rotation. But the scroll events looked exactly like mouse scroll events, so if you really did a mouse scroll and you also use the trackpad then it just ignored the scroll event. I see this problem described in the ChimeraX 1.6 code here > > https://github.com/RBVI/ChimeraX/blob/6e2f12a093d52c317a4f8aaa1070334dcfe6f5... > > ''' > macOS generates mouse wheel events in response to a two-finger drag on trackpad. > We discard those if we have multitouch trackpad support enabled so that 2-finger > drag should be rotation. But we don't want to discard wheel events that come > from a non-trackpad device. Unfortunately macOS and Qt5 provides no way to distinguish > magic mouse scroll from a trackpad scroll, both are reported as synthesized events > and there is no source device id available. If there are any trackpad devices and > multitouch is enabled then the magic mouse wheel events are thrown away. This > is ChimeraX bug #1474. We used to instead see if we recently received a touch event > and in that case throw away any wheel event. Unfortunately on macOS we sometimes > don't get touch events after clicking in the Log or other windows and then moving > back to the graphics window, until the second multitouch drag is done. > ''' > > The ChimeraX daily build and 1.7 release candidate changed this code using a newer Qt window toolkit capability to distinguish the two-finger drag from a mouse scroll wheel. Mouse scroll is working for me in those newer ChimeraX version and it does not work after I use a two finger rotation on the trackpad with ChimeraX 1.6. So use the newer ChimeraX. > > Tom > > On Nov 8, 2023, at 7:28 PM, Dale Calleja via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hello, > > I am currently learning to use ChimeraX (v1.6.1) and I am having issues with my scroll wheel. I notice when I first open the software using the scroll wheel on my mouse will zoom in and out of the structure but, after some time it simply stops working and the scroll wheel does nothing. > > Is this a button I am accidentally pressing or have I discovered a bug? It doesn’t seem to have any pattern, I am just clicking around changing the display of my protein. > > Thanks! > > Dale. > > Dale Calleja > > PhD Student, Komander Lab > > Ubiquitin Signalling Division > > WEHI > > 1G Royal Parade > > Parkville VIC 3052 > > Australia > > Email calleja.d(a)wehi.edu.au <mailto:calleja.d@wehi.edu.au> > > Walter and Eliza Hall Institute of Medical Research > > 1G Royal Parade Parkville Victoria 3052 Australia > > www.wehi.edu.au <https://wehi.edu.au/> > > Twitter <https://twitter.com/WEHI_research> | Facebook <https://www.facebook.com/WEHIresearch/> | Instagram <https://www.instagram.com/wehi_research> | Youtube <https://www.youtube.com/user/WEHImovies> | LinkedIn <https://www.linkedin.com/company/wehi_research> > > WEHI acknowledges the Wurundjeri people of the Kulin Nation as the traditional owners of the land where our campuses are located and the continuing connection to country and community. > > Private and confidential > > The content of this e-mail and any attachments may be private and confidential, intended only for use of the individual or entity named. If you are not the intended recipient of this message you must not read, forward, print, copy, disclose, use or store in any way the information this e-mail or any attachment contains. If you are not the intended recipient, please notify the sender immediately and delete or destroy all copies of this e-mail and any attachment. > > _______________________________________________ > > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> > > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> > > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ > > ######################## _______________________ Ján Bíňovský, Ph.D. Postdoctoral Scientist Bacteriophages [/Users/sonja/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1037324061]<https://www.biochem.mpg.de/de> MAX PLANCK INSTITUTE OF BIOCHEMISTRY Am Klopferspitz 18 | 82152 Martinsried | Germany Phone: +49 (0) 8578 - 3049 binovsky(a)biochem.mpg.de<mailto:binovsky@biochem.mpg.de> www.biochem.mpg.de<http://www.biochem.mpg.de/> [cid:CC515546-C3CA-41D9-AB54-BFF5FC6CE713]<https://twitter.com/mpi_biochem?lang=de> [signature_1936393271]<https://de.linkedin.com/company/max-planck-institute-of-biochemistry> [signature_138060577]<https://www.facebook.com/biochem.mpg.de/>

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