A stereo image is generated by drawing two images from two different perspectives, one from the left eye and one from the right. The images are made by finding the view that would be seen by someone located inside the scene. The method uses two parameters to find the view; the eye separation and the focal length. The first defines the distance between the eyes and gives the parallax effect. Setting the separation to 0 will result in a flat 2D image, while setting it too large will give most people a headache.
The graphics model used by VMD assumes the eyes looking in front of the viewer and focusing at the same point the focal length away. If the focal length is 0, the viewer's eyes are crossed and looking at each other. A larger focal length will often help in creating a viewable image.
The two parameters can be changed with the text commands display focallength and display eyesep, or using the Display form.
In general, try to make the eye separation as large as possible without giving the viewer a migrane, and try to vary the focal length to cut down on double images. It may often help to translate the molecule forward or backward and also adjust the scaling, since there is typically an optimum position for a molecule for a given set of stereo parameters.