ChimeraX Detection

echidna auto-detects ChimeraX on all supported platforms. You can also specify the path manually.

Resolution Priority

ChimeraX path is resolved in this order:

1. CLI flag: --chimerax /path/to/ChimeraX
2. Environment variable: CHIMERAX_PATH=/path/to/ChimeraX
3. Project config: chimerax_path in echidna.toml
4. Auto-detection: Platform-specific default paths

Auto-Detection Paths

macOS

Path	Source
/Applications/ChimeraX.app/Contents/MacOS/ChimeraX	Standard install
~/Applications/ChimeraX.app/Contents/MacOS/ChimeraX	User install

Also searches PATH for chimerax and ChimeraX.

Linux

Path	Source
/usr/bin/chimerax	DEB/RPM symlink
/usr/local/bin/chimerax	Manual install
/usr/lib/ucsf-chimerax/bin/ChimeraX	DEB package (Ubuntu/Debian)
/usr/libexec/UCSF-ChimeraX/bin/ChimeraX	RPM package (RHEL/Rocky/CentOS)
~/.local/bin/chimerax	User install

Windows

Path	Source
C:\Program Files\ChimeraX\bin\ChimeraX-console.exe	Standard install
C:\Program Files\ChimeraX\bin\chimerax.exe	Alternative name
C:\Program Files\ChimeraX 1.x\bin\ChimeraX-console.exe	Legacy versioned install (pre-1.7)

For legacy installs, echidna scans C:\Program Files for directories matching ChimeraX <version> and tries the newest version first.

Manual Configuration

Using the CLI Flag

echi run --chimerax /custom/path/to/ChimeraX

This flag is available on all commands (it's a global option).

Using an Environment Variable

export CHIMERAX_PATH=/custom/path/to/ChimeraX
echi run

Using echidna.toml

chimerax_path = "/custom/path/to/ChimeraX"

Flatpak Installations

Flatpak installations are not auto-detected because they require flatpak run instead of direct execution. To use a Flatpak ChimeraX:

1. Create a wrapper script:

   #!/bin/bash
   flatpak run edu.ucsf.rbvi.ChimeraX "$@"

2. Save it as chimerax somewhere on your PATH (e.g., ~/.local/bin/chimerax)
3. Make it executable: chmod +x ~/.local/bin/chimerax