Setting ChimeraX as the default 3D Structure Viewer

Jalview supports Jmol, Pymol, Chimera and ChimeraX 3D molecular structure viewers. Jmol is the default viewer, however, Chimera can be set up as the default choice from Preferences.

  1. First, ChimeraX must be downloaded and installed on the computer. ChimeraX program is available on the UCSF website

  2. In the desktop menu, select Jalview $\Rightarrow$ Preferences. In the ‘Structure’ tab set Default structure viewer as CHIMERAX, then click OK.

  3. Close the entire Jalview program, by selecting Jalview $\Rightarrow$ Quit Jalview from the desktop menu. Then relaunch Jalview, Chimera should open as the default 3D viewer.

If this does not work then you may need to set the Path to ChimeraX program in Preferences. Such as /Volumes/MacintoshHD/Applications/

Note: The Jmol structure viewer sits within the Jalview desktop, however, the Chimera structure viewer sits outside the Jalview desktop.

For more information on this topic go to section 7.1 of the Jalview manual.
 This exercise can be viewed in the 3D Molecular Structure Jmol and UCSF Chimera viewers video.