Am I interpreting these images correctly that the atoms themselves aren't truly visible and the hexagonal lines trace the outline of the bonds between them? (in which case the atoms would be located at the intersections of those lines). Which would be interesting if that were the case, because in some of those images there are curved "bubbles" that bend outwards to locations where there should be additional atoms but nothing is actually there. It would be even more interesting to see a new atom or molecule fall into that slot and watch how the structure changes as the energy levels rearrange themselves.
One of the things they are trying to investigate is why those bonds aren't always straight lines. Fascinating stuff. There is the world we see, and then the strange, alien world that exists at the molecular/atomic/quantum level.