Bonds

Nearly everything about this option is the same as lines except that instead of drawing a bond as a line between two atoms, a cylinder is drawn instead. To be more specific, it draws an $n$-sided prism, where the number of sides is determined in the Graphics form by the ``Bond Res'' control and the radius is given by the value of ``Bond Rad,'' in Angstroms. If the radius or number of sides gets too small, the bonds are drawn as lines.

In order to fine tune the bond representation, VMD does a small amount of trickery to the prisms. That is, imagine two hollow cylinders coming together so that the center of the face of one cylinder is in the same position as the center of the face of the other cylinder. Also suppose these two cylinders come together at 90 degrees. Although most of these two cylinders will overlap, there will appear to be a gap at their intersection.

To correct for this problem, VMD extends both cylinders somewhat so that the far ends touch. If one looks closely, this produces more of an overlap, but it is much nicer looking than the gap. When three or more bonds join at one atom, VMD chooses the lowest numbered bond and extends all other bonds to meet with that one. It then extends that lowest numbered bond to meet with the second lowest numbered one. A bit technical, but not too difficult to do.