You can make some modifications to the display of your molecule using a pop-up menu. This menu will appear when you click with the left mouse button, and hold. The commands in the pop-up menu depend on the object you click on.
Click on a C-atom with the left mouse button, and keep pressed down without moving
The following menu appears:
Choose the Atom Popup → Set C Color menu command
A color select box will appear:
Select a new color and click OK
You have changed the color of the carbon atoms. All atoms of the same type, in this case carbon, will always have the same color.
