Since I just finished up an ebuild for the next-generation application of what I do all day, I thought you might like to see what it looks like. What you’re seeing is a zoomed-in picture of part of a protein. The electron density is in blue, and green and red indicate where there’s too little or too much actual atom present for the density. The big cross things are waters.
The atom bonds in the pic look a little jagged because I haven’t gotten its antialiasing working yet (works fine on OS X, FWIW).
Keep in mind this is pretty much state of the art in my field — it’s using gtk-1 and glut rather than tcltk, or home-rolled widgets.
The program is called coot. Unfortunately, it won’t enter the tree until I fix rpath issues with ccp4, a huge bundle of apps that this depends on.