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.