Experimental UCSF ChimeraX Flatpak

Flatpak applications can be installed on a wide variety of Linux variants. We are experimenting with a flatpak build of ChimeraX to make ChimeraX more widely available. But we are new to the flatpak ecosystem, so any feedback you have will be helpful. Please send feedback by using ChimeraX's "Report a Bug" dialog (preferred because it tells us about your computer's configuration), or send feedback directly to Greg Couch.

Installation Instructions

Install the flatpak package and command
You need system administrator priviledges to install the flatpak package. Go to flatpak.org, click on Get Setup, select the icon for your variant of Linux, and follow those instructions.
Optionally configure flatpak's flathub repository
If you didn't configure flatpak to use the flathub repository during the previous step, do it now:
flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
Optional per-user flathub repository
The default instructions from flathub.org are for installing for all users. If you are going to install ChimeraX just for yourself, you need to add a per-user flathub repository with:
flatpak remote-add --user --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
Download ChimeraX flatpak
During this test phase, download ChimeraX.flatpak. It corresponds to a release candidate build from 14 December 2023. Later you will get the ChimeraX flatpak from the Linux sections of the download page.
Install ChimeraX flatpak
For all users:
sudo flatpak install Chimerax.flatpak
For just yourself (assuming per-user flathub repository is installed as shown above):

flatpak install --user Chimerax.flatpak

Running ChimeraX

After ChimeraX is installed, your desktop environment should provide an icon or menu entry to run ChimeraX. You can also run ChimeraX in a terminal window with:

flatpak run edu.ucsf.rbvi.ChimeraX

And if you do that a lot, create an alias. For example, for sh and bash:

alias chimerax='flatpak run edu.ucsf.rbvi.ChimeraX'

Then to run ChimeraX, simply give the command chimerax.

Binary Compatibility

The test ChimeraX.flatpak is not binary compatible with the regular Linux builds. That will be fixed when the flatpak builds are integrated with our build system. If you need binary compatibility or a newer daily build, you can replace the chimerax directory, app/edu.ucsf.rbvi.ChimeraX/current/active/files/lib/python3.11/site-packages/chimerax, with the version from any Linux daily build from July 13, 2023 or later. For per-user installations, that directory is ~/.local/share/flatpak. The system location varies depending on the Linux variant, and is given by the output from flatpak --installations. How to extract the chimerax directory from a .deb or .rpm package is left as an exercise for the user.

ChimeraX Flatpak Permissions

Flatpak applications have to state what permissions they need to run. The Flatseal flatpak application can be used to see and modify what permissions an application uses.

ChimeraX uses:

• share=ipc, socket=x11, socket=wayland: For GUI access (X11/Wayland).
• device=dri: For hardware accelerated graphics.
• share=network: For network access to download data files, check for updates, etc.
• filesystem=xdg-cache/ChimeraX:create, filesystem=xdg-config/ChimeraX:create, filesystem=xdg-data/ChimeraX:create, filesystem=xdg-download/ChimeraX:create: Per-user cache and configuration data for backwards and forwards compability with other versions of ChimeraX.
• filesystem=xdg-desktop: Allow the ChimeraX "Spin Movie" Toolbar icon to write the movie to the Desktop folder.
• filesystem=home: Allow all files in home directory to be accessed. This permission extends the previous filesystem= permissions.
• filesystem=host: Allow practically all files on the computer to be accessed. For example, this means a data file in /var/tmp can be opened or written. This permission extends the previous filesystem= permissions.

filesystem=home, filesystem=host, and filesystem=xdg-desktop can be safely turned off with Flatseal for various levels of sandboxing ChimeraX.

ChimeraX's virtual reality code has not been tested in the flatpak environment and may require additional permissions.

ChimeraX Flatpak Troubleshooting

Common errors and their solutions:

error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires the runtime org.freedesktop.Platform/x86_64/22.08 which was not found
This means that flatpak hasn't been configured to use the flathub repository yet. See the installation instructions.
BUG: ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory
libQt6Core.so is part of the ChimeraX release, but it is not loaded if the system's Linux kernel is too old. ChimeraX uses the Qt user interface toolkit, which requires that the Linux kernel be version 3.11 or newer. The kernel version is shown by the output from the uname -r command.