Hi,

I'd like to request options for the molecule tool which allow to customize more the appearance.

Atom sizes: either same sphere radius for all atoms, the covalent radius, or the atomic radius. These are the settings VisIt has.
Bond radii: increase/decrease. Turn off (bond radius 0)
Atom coloring choices: cpk_jmol, amino_shapely, amino_rasmol are good coloring sets. (see e.g. VisIt).

Sebastian