The appearance of the atom may be changed by either changing the atom pattern or the shading of the atom. You may also change the radius of each atom by using a resource editor and editing the resources of type "ATOM" and changing the radius. The latter may only be done external to the program, while the other two can be done within the program. You may also edit the patterns in a resource editor.
The patterns remain the same from molecule to molecule and the resource for the patterns is kept with the program.