Stick diameter is the width of bonds in stick mode in Angstroms.
Ball radius is the size of atom spheres in Ball draw type, measured in Angstroms.
Fine Build Fine Clean3D builds up conformers of fragments to find low energy conformer. Leaves failed fragments intact.
Fine with Hydrogenize The build process always adds explicit Hydrogens to the structures which are removed if not present in the original molecule. This option prevents the removal of extra Hydrogen atoms, otherwise gives the same results than Fine build.
Fast Build Fast clean, which if fails, performs fine clean. It accepts any generated structure, and it is the default behavior of the Clean3D function.
Build or Optimize Builds 3D structure for non-3D molecules and just optimizes the 3D molecules with the Dreiding force field.
Gradient Optimize Optimizes with the Dreiding force field using the actual structure as starting geometry.