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RBVI / ChimeraX

Source code for molecular graphics program UCSF ChimeraX
https://www.rbvi.ucsf.edu/chimerax/
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Fedora 41: Flatpack doesnt show settings or tool shed window #48

Open aretaon opened 19 hours ago

aretaon commented 19 hours ago

Description of the issue

I installed ChimeraX 1.8 on Fedora 41 using flatpak (see log below). The application starts and looks okay, however, I cannot open new windows (e.g. when clicking on Favorites -> Settings or on Tools -> More Tools, nothing happens). The same is true for the rpm-Version. Potential suspect might be my graphics card which is an AMD Radeon™ RX 640 with open source kernel drivers and the windowing system is Wayland.

Logs

Installation

sudo flatpak install ChimeraX-1.8.flatpak

edu.ucsf.rbvi.ChimeraX permissions: ipc network wayland x11 dri file access [1]

[1] home, host, xdg-cache/ChimeraX:create, xdg-config/ChimeraX:create,
    xdg-data/ChimeraX:create, xdg-desktop, xdg-download/ChimeraX:create

    ID                               Branch           Op           Remote                   Download
  1. [✓] edu.ucsf.rbvi.ChimeraX master i chimerax-origin 0 bytes

Installing… Note that '/var/lib/flatpak/exports/share' is not in the search path set by the XDG_DATA_HOME and XDG_DATA_DIRS environment variables, so applications may not be able to find it until you set them. The directories currently searched are:

  • /root/.local/share ID Branch Op Remote Download
    1. [✓] edu.ucsf.rbvi.ChimeraX master i chimerax-origin 0 bytes

Installation complete.

Application start

flatpak run edu.ucsf.rbvi.ChimeraX 
Gtk-Message: 13:24:45.383: Failed to load module "canberra-gtk-module"
Gtk-Message: 13:24:45.383: Failed to load module "pk-gtk-module"
Gtk-Message: 13:24:45.384: Failed to load module "canberra-gtk-module"
Gtk-Message: 13:24:45.384: Failed to load module "pk-gtk-module"
NOTE: available bundle cache has not been initialized yet
gregcouch commented 10 hours ago

I'll spin up a Fedora 41 virtual machine and check. If I had to guess from your description, the problem is most likely ChimeraX's use of Wayland (via the Qt UI libraries). And the solution might be ChimeraX 1.10 :-(. The open source AMD drivers are generally excellent. Switching from Wayland to X11, depends on what display manager you're using -- for gdm, edit /etc/gdm3/custom.conf and add "WaylandEnable=false".

gregcouch commented 4 hours ago

The ChimeraX 1.8 flatpak works using Wayland in a Fedora 41 virtual machine. The VM was initially using Mesa 24.2.4. After updating, to Mesa 24.2.7, it still works.

So maybe it is the graphics driver. Make sure your system is fully patched. If there is a proprietary driver from AMD, you could try that instead of the open source Mesa driver.

I tried not using Wayland by editing /etc/gdm/custom.conf, and that didn't work. I had to stop and disable the gdm service. Then install lightdm, and enable and start it.