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.

Show Bond in Hand when checked, bond types are shown under the mouse cursor like template structures.

Show Lone Pair as Line when checked, lone pairs on the canvas are shown as lines.

Show Charge in Circle when checked, a circle is displayed around the charge.

Fog effect factor: manual setting of the fading strength. No fog: all regions of the structure is displayed with the same line strength and color. Strong effect: the fading is at its maximum (molecule is only slightly visible at the far end).