RedHat Enterprise Linux 10 has dropped Xorg in favor of Wayland, and Fedora 43 will likely do the same. Fedora 42 already uses Wayland by default. Is Chimera expected to work with Wayland? ChimeraX works fine in our environment with Wayland, but I have folks that still want to use Chimera. And they're getting a Togl failure at startup: "Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions." I would love to tell them that "the Chimera folks say it doesn't work with Wayland so you need to switch to ChimeraX" (we can eke out another six months or so with Fedora 42 using Xorg) but if you think it *should* work, any clues as to where to look to tweak our configuration? Other than using the NVIDIA drivers (570.133.07), we are using a stock Fedora and Wayland install.
Hi Ben, I think your wish will come true that Chimera is not going to work directly on Wayland, and Chimera users should move to ChimeraX if they want to work on modern computer operating systems. Chimera uses the Tk window toolkit for its user interface, an ancient package popular around 2000, and so it is probably easiest to explore if Tk can work with Wayland. Googling Tk Wayland says "Tk, the toolkit underlying Tkinter, does not have native Wayland support. Instead, Tk applications run under XWayland, a compatibility layer that allows X11 applications to run on Wayland compositors." Tkinter is the Python bindings for Tk and is what Chimera is using. Even if Tk could work directly with Wayland without XWayland, Chimera still may not work because Chimera needs OpenGL 3D graphics support and Togl is a Tk extension for making an OpenGL window that is even much less well supported than Tk. I don't know if Togl will work with XWayland. Let us know if you figure anything out, good or bad. We have had no funding for Chimera development for about 10 years, all the funding, development and support is for ChimeraX. So we won't be undertaking any major work to make Chimera work on Wayland. Tom
On Jun 2, 2025, at 5:45 PM, Ben Webb via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
RedHat Enterprise Linux 10 has dropped Xorg in favor of Wayland, and Fedora 43 will likely do the same. Fedora 42 already uses Wayland by default. Is Chimera expected to work with Wayland?
ChimeraX works fine in our environment with Wayland, but I have folks that still want to use Chimera. And they're getting a Togl failure at startup: "Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions." I would love to tell them that "the Chimera folks say it doesn't work with Wayland so you need to switch to ChimeraX" (we can eke out another six months or so with Fedora 42 using Xorg) but if you think it *should* work, any clues as to where to look to tweak our configuration? Other than using the NVIDIA drivers (570.133.07), we are using a stock Fedora and Wayland install. _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
Hi Tom - yes, I would certainly not expect Chimera to natively support Wayland (it predates it, after all). And I wouldn't spend much time myself (or expect you to either) trying to make it work - unless a bunch of folks tell me that it works fine for them, so clearly I am holding it wrong! In my testing so far most X11 applications work fine with XWayland, including VMD for example. So I think Togl is the sticking point here. The underlying error comes from Togl and is "couldn't choose pixel format" and "Couldn't configure togl widget". XCrySDen also uses Togl and reports the same error with Wayland, but some folks have a workaround: https://unix.stackexchange.com/questions/702305/running-xcrysden-in-wayland. I'm not familiar enough with Tcl though to know whether that workaround would also work for Chimera or even where to inject it in the Chimera startup. On Mon, Jun 2, 2025 at 6:37 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Ben,
I think your wish will come true that Chimera is not going to work directly on Wayland, and Chimera users should move to ChimeraX if they want to work on modern computer operating systems.
Chimera uses the Tk window toolkit for its user interface, an ancient package popular around 2000, and so it is probably easiest to explore if Tk can work with Wayland. Googling Tk Wayland says "Tk, the toolkit underlying Tkinter, does not have native Wayland support. Instead, Tk applications run under XWayland, a compatibility layer that allows X11 applications to run on Wayland compositors." Tkinter is the Python bindings for Tk and is what Chimera is using. Even if Tk could work directly with Wayland without XWayland, Chimera still may not work because Chimera needs OpenGL 3D graphics support and Togl is a Tk extension for making an OpenGL window that is even much less well supported than Tk. I don't know if Togl will work with XWayland.
Let us know if you figure anything out, good or bad. We have had no funding for Chimera development for about 10 years, all the funding, development and support is for ChimeraX. So we won't be undertaking any major work to make Chimera work on Wayland.
Tom
On Jun 2, 2025, at 5:45 PM, Ben Webb via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
RedHat Enterprise Linux 10 has dropped Xorg in favor of Wayland, and Fedora 43 will likely do the same. Fedora 42 already uses Wayland by default. Is Chimera expected to work with Wayland?
ChimeraX works fine in our environment with Wayland, but I have folks that still want to use Chimera. And they're getting a Togl failure at startup: "Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions." I would love to tell them that "the Chimera folks say it doesn't work with Wayland so you need to switch to ChimeraX" (we can eke out another six months or so with Fedora 42 using Xorg) but if you think it *should* work, any clues as to where to look to tweak our configuration? Other than using the NVIDIA drivers (570.133.07), we are using a stock Fedora and Wayland install. _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
Hi Ben, I just tried Chimera 1.19 (the current version) on Wayland on Ubuntu 24.04 and it rendered atomic models fine. Also ChimeraX worked fine. One glitch was that using Wayland I got the Mesa graphics driver instead of the Nvidia RTX 4090 graphics driver when I use Xorg on that same machine. That makes rendering sluggish. Posts online suggests that the nvidia driver may not be working on Wayland because of SecureBoot which is enabled on the test machine. I did not try to monkey around with SecureBoot and driver signing to get the nvidia driver to work. So if you find Chimera not working on Wayland then perhaps it really has to do with the graphics driver on your Wayland test system is broken, or lacking in basic rendering capabilties that Chimera requires. Tom
On Jun 2, 2025, at 8:19 PM, Ben Webb via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Tom - yes, I would certainly not expect Chimera to natively support Wayland (it predates it, after all). And I wouldn't spend much time myself (or expect you to either) trying to make it work - unless a bunch of folks tell me that it works fine for them, so clearly I am holding it wrong!
In my testing so far most X11 applications work fine with XWayland, including VMD for example. So I think Togl is the sticking point here. The underlying error comes from Togl and is "couldn't choose pixel format" and "Couldn't configure togl widget". XCrySDen also uses Togl and reports the same error with Wayland, but some folks have a workaround: https://unix.stackexchange.com/questions/702305/running-xcrysden-in-wayland. I'm not familiar enough with Tcl though to know whether that workaround would also work for Chimera or even where to inject it in the Chimera startup.
On Mon, Jun 2, 2025 at 6:37 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Ben,
I think your wish will come true that Chimera is not going to work directly on Wayland, and Chimera users should move to ChimeraX if they want to work on modern computer operating systems.
Chimera uses the Tk window toolkit for its user interface, an ancient package popular around 2000, and so it is probably easiest to explore if Tk can work with Wayland. Googling Tk Wayland says "Tk, the toolkit underlying Tkinter, does not have native Wayland support. Instead, Tk applications run under XWayland, a compatibility layer that allows X11 applications to run on Wayland compositors." Tkinter is the Python bindings for Tk and is what Chimera is using. Even if Tk could work directly with Wayland without XWayland, Chimera still may not work because Chimera needs OpenGL 3D graphics support and Togl is a Tk extension for making an OpenGL window that is even much less well supported than Tk. I don't know if Togl will work with XWayland.
Let us know if you figure anything out, good or bad. We have had no funding for Chimera development for about 10 years, all the funding, development and support is for ChimeraX. So we won't be undertaking any major work to make Chimera work on Wayland.
Tom
On Jun 2, 2025, at 5:45 PM, Ben Webb via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
RedHat Enterprise Linux 10 has dropped Xorg in favor of Wayland, and Fedora 43 will likely do the same. Fedora 42 already uses Wayland by default. Is Chimera expected to work with Wayland?
ChimeraX works fine in our environment with Wayland, but I have folks that still want to use Chimera. And they're getting a Togl failure at startup: "Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions." I would love to tell them that "the Chimera folks say it doesn't work with Wayland so you need to switch to ChimeraX" (we can eke out another six months or so with Fedora 42 using Xorg) but if you think it *should* work, any clues as to where to look to tweak our configuration? Other than using the NVIDIA drivers (570.133.07), we are using a stock Fedora and Wayland install. _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
Hi Tom, thanks for checking this on your system. Sounds like NVIDIA is the culprit then - their support for Wayland has been lagging for a while. Chimera works fine for me too on Fedora when using the Nouveau driver with Wayland. It is only when using the NVIDIA driver with Wayland that we see the failure (although Chimera with NVIDIA and Xorg works fine, and ChimeraX works fine with NVIDIA with both Xorg and Wayland). For reference this is with both versions 570.133.07 and 570.153.02 of the NVIDIA driver. The NVIDIA driver works fine with SecureBoot and Wayland (just not with Chimera), so I don't think we can blame SecureBoot. The kernel module just needs to be signed with a suitable key (and we have that set up on our systems). If you can get the NVIDIA driver to work on your Ubuntu box it would be interesting to see if you get the same failure. Otherwise I can probably do it. On Tue, Jun 3, 2025 at 3:28 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Ben,
I just tried Chimera 1.19 (the current version) on Wayland on Ubuntu 24.04 and it rendered atomic models fine. Also ChimeraX worked fine. One glitch was that using Wayland I got the Mesa graphics driver instead of the Nvidia RTX 4090 graphics driver when I use Xorg on that same machine. That makes rendering sluggish. Posts online suggests that the nvidia driver may not be working on Wayland because of SecureBoot which is enabled on the test machine. I did not try to monkey around with SecureBoot and driver signing to get the nvidia driver to work.
So if you find Chimera not working on Wayland then perhaps it really has to do with the graphics driver on your Wayland test system is broken, or lacking in basic rendering capabilties that Chimera requires.
Tom
On Jun 2, 2025, at 8:19 PM, Ben Webb via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Tom - yes, I would certainly not expect Chimera to natively support Wayland (it predates it, after all). And I wouldn't spend much time myself (or expect you to either) trying to make it work - unless a bunch of folks tell me that it works fine for them, so clearly I am holding it wrong!
In my testing so far most X11 applications work fine with XWayland, including VMD for example. So I think Togl is the sticking point here. The underlying error comes from Togl and is "couldn't choose pixel format" and "Couldn't configure togl widget". XCrySDen also uses Togl and reports the same error with Wayland, but some folks have a workaround: https://unix.stackexchange.com/questions/702305/running-xcrysden-in-wayland. I'm not familiar enough with Tcl though to know whether that workaround would also work for Chimera or even where to inject it in the Chimera startup.
On Mon, Jun 2, 2025 at 6:37 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Ben,
I think your wish will come true that Chimera is not going to work directly on Wayland, and Chimera users should move to ChimeraX if they want to work on modern computer operating systems.
Chimera uses the Tk window toolkit for its user interface, an ancient package popular around 2000, and so it is probably easiest to explore if Tk can work with Wayland. Googling Tk Wayland says "Tk, the toolkit underlying Tkinter, does not have native Wayland support. Instead, Tk applications run under XWayland, a compatibility layer that allows X11 applications to run on Wayland compositors." Tkinter is the Python bindings for Tk and is what Chimera is using. Even if Tk could work directly with Wayland without XWayland, Chimera still may not work because Chimera needs OpenGL 3D graphics support and Togl is a Tk extension for making an OpenGL window that is even much less well supported than Tk. I don't know if Togl will work with XWayland.
Let us know if you figure anything out, good or bad. We have had no funding for Chimera development for about 10 years, all the funding, development and support is for ChimeraX. So we won't be undertaking any major work to make Chimera work on Wayland.
Tom
On Jun 2, 2025, at 5:45 PM, Ben Webb via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
RedHat Enterprise Linux 10 has dropped Xorg in favor of Wayland, and Fedora 43 will likely do the same. Fedora 42 already uses Wayland by default. Is Chimera expected to work with Wayland?
ChimeraX works fine in our environment with Wayland, but I have folks that still want to use Chimera. And they're getting a Togl failure at startup: "Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions." I would love to tell them that "the Chimera folks say it doesn't work with Wayland so you need to switch to ChimeraX" (we can eke out another six months or so with Fedora 42 using Xorg) but if you think it *should* work, any clues as to where to look to tweak our configuration? Other than using the NVIDIA drivers (570.133.07), we are using a stock Fedora and Wayland install. _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
On 6/2/25 5:45 PM, Ben Webb wrote:
RedHat Enterprise Linux 10 has dropped Xorg in favor of Wayland, and Fedora 43 will likely do the same. Fedora 42 already uses Wayland by default. Is Chimera expected to work with Wayland?
ChimeraX works fine in our environment with Wayland, but I have folks that still want to use Chimera. And they're getting a Togl failure at startup: "Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions."
Following up for others in the same situation: there is a simple workaround to make Chimera work on Linux with Wayland and the NVIDIA drivers: simply edit share/OpenGLDebug/__init__.py and change the line that reads graphics = Togl.Togl(parent, width=1, height=1) to instead read graphics = Togl.Togl(parent, width=1, height=1, double=True) i.e. the failure appears to be due a lack of support for single-buffered windows. But fortunately the main Chimera window is double-buffered anyway, so it's only the initial graphics check that was failing. Ben
This seems like a fairly harmless change, so I have added it to the Chimera code. In the daily build only (starting tomorrow). --Eric
On Jun 9, 2025, at 11:01 AM, Ben Webb via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
On 6/2/25 5:45 PM, Ben Webb wrote:
RedHat Enterprise Linux 10 has dropped Xorg in favor of Wayland, and Fedora 43 will likely do the same. Fedora 42 already uses Wayland by default. Is Chimera expected to work with Wayland? ChimeraX works fine in our environment with Wayland, but I have folks that still want to use Chimera. And they're getting a Togl failure at startup: "Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions."
Following up for others in the same situation: there is a simple workaround to make Chimera work on Linux with Wayland and the NVIDIA drivers: simply edit share/OpenGLDebug/__init__.py and change the line that reads
graphics = Togl.Togl(parent, width=1, height=1)
to instead read
graphics = Togl.Togl(parent, width=1, height=1, double=True)
i.e. the failure appears to be due a lack of support for single-buffered windows. But fortunately the main Chimera window is double-buffered anyway, so it's only the initial graphics check that was failing.
Ben _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
participants (3)
-
Ben Webb -
Eric Pettersen -
Tom Goddard