I played around a little bit trying to make the vectors & boxes look
better. I tried making them transparent thinking that they would look like
they passed into the atom. But I wasn't very pleased with the results, so
I didn't check it in.
I changed the atom vibrational vectors so that they show up behind the
atom when you rotate the molecule. Before they were always painted on top
of the atom.
For the crystal box I changed the z-order so that the lines are painted a
bit later (the least-negative of the two endpoints). You can see this on
bulk_Si where now the three lines of the crystal box are now visible all
Q: Is there some time of more fancy rendering style that would be useful
for these vectors and/or crystal box outlines?