I was shocked when I learned that while scientist have been taking pictures of atoms for years now, they've only recently been able to take pictures of molecules (a group of attached atoms, to make the distinction).
The problem is that electron microscopes bombard the molecules with electrons, disrupting and then breaking apart the weaker bonds between atoms, when taking their pictures. Now with newer microscope technology (something like an x-ray, from the article), we can take a picture of a whole molecule because we aren't breaking them apart.
There's a high power (electron microscope maybe? but I'm not sure) microscope at my university. A couple of years ago I got the chance to be the lab and see the 'photos' on the monitor as they were doing research.
The sights were really boring to me and the readouts made no sense, but the idea of what I was seeing got me all giddy.