I think that I have found a problem with the rendering of semi-opaque surfaces in threejs : some portions of semi-opaque surfaces that should be rendered as if seen "through" other semi-opaque surfaces "snap" in and out of existence when the graph is rotated or rescaled.
This is much more easily shown than explained. Run the attached Jupyter notebook worksheet (after scannig it with your favorite anti-virus software...) : it allows to compare the behaviour of jmol (sjow and not-so-clean, but correct) and threejs (faster, smoother, but scarce in details and sometimes just plain wrong).
This is *not* reported on Trac (at least, none of the 28 tickets (4 open) retrieved by a search on "threejs" treat it).
Is it ticket-worthy ?