Now you see a GC base pair, cut through the plane where the three Watson-Crick hydrogen bonds are. Notice how the DNA rises and falls as it rotates around the center of mass, which includes the invisible protein. This is because each representation on the Display Menu turns off all other representations for the selected atoms. In contrast, when representations are applied from the command line, they do not turn off other representations. Be sure to include the decimal point after the one, which makes RasMol interpret it as Angstroms.
Balls are spacefill with a uniform radius.
Now click on a few atoms. Now you need to translate to the left to center the image. By default, you get cross-eyed stereo. Viewing stereo takes practice, can be hard on the eyes, and is not necessary for most purposes. Rotation without stereo gives you an excellent perception of major 3D relationships.