Quoting an Ubuntu user:
All atomic species are readily identifiable in the display window of gdis. In case two atoms share a similar colour, this could be changed using the Periodic Table tool.
Gdis will display castep output file with several atomic species using only one "atom". Using the periodic table tool to change the colour of the "inactive" atom will render no change, while changing the colour of the active atom will change the colour of all atoms.