Ball radius

Size of atom spheres in Ball draw type, measured in Angstroms.

Bond radius

Size of bond cylinders in Ball and Stick draw type, measured in Angstroms.

Stick radius

Size of bond cylinders in Stick draw type, measured in Angstroms.

Line width

Width of bonds in wire mode.

Double bond distance

Gap between two lines/sticks representing a double bond. It is determined as a percentage of Bond radius.

Double bond width

Thickness of line/stick representing a double bond. It is expressed relative to the thickness of a single bond.

Display bond order

When checked double bonds are drawn by two line segments, otherwise all bonds are represented as single bonds.
Future releases will introduce drawing mode for triple and aromatic bonds too.

vdW scaled balls

When checked atom spheres in Ball and Ball-and-Stick modes are scaled according to their van der Waals radii. Otherwise all atoms (apart from hydrogen) are represented by uniform sphere radii. Hydrogen radius is half of atom radius.

Smooth colored sticks

When checked bi-colored stick bonds are colored gradually from one color to the other (in CPK atom coloring mode). Otherwise the two halves are draw with the two different colors.