B9: How to see in stereo.
This feature of Jmol displays two images on the screen. The images are slightly rotated with respect to each other such that when they are merged by using colored (red/green) glasses, or crossing your eyes (cross-eyed), or relaxing your eyes (wall-eyed), you can see the molecule in 3D. Most people can accomplish cross-eyed viewing. Wall-eyed viewing is similar to the "magic eye" viewing. Pick which ever is most comfortable for you.

To turn on the stereo image:

Style ¬ Stereographic ¬ Cross-eyed viewing

You now see two images, and if you cross your eyes you should be able to form a single 3D image.