Thank you for fixing the Z intersection of the orbecules, C3lt1c!
One other thing, which is technical and not really about the visuals (it looks fine now) - You seem to be calling glGenBuffers for every single orbecule (sometimes even twice for a single orbecule!). This results in 100's of allocated VBO's.
Maybe you can allocate one buffer and put all the vertexes and colors in there, and then do multiple glDrawElements?
Just a little coder tip!
