UCSF ChimeraX Flatpaks

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

ChimeraX 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:
sudo 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
If you haven't already, download a ChimeraX flatpak from the Linux sections of the download page.
Install ChimeraX flatpak
Install for all users:
sudo flatpak install ChimeraX.flatpak
Or, for just yourself (install per-user flathub repository first as shown above in #3):

flatpak install --user ChimeraX.flatpak
(Use name of downloaded .flatpak file instead of ChimeraX.flatpak.)

Running ChimeraX from a Terminal Window

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. (Use edu.ucsf.rbvi.ChimeraX-daily or edu.ucsf.rbvi.ChimeraX-techpreview if using a daily or techpreview release.)

Note: several warnings will appear in the terminal window and can be ignored. In particular, the Gtx messages about failing to load a module, and the path override failures for base::DIR_APP_DICTIONARIES.

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. The only solution is to update the kernel used, which is usually done by upgrading the system to a newer version.