PyMOL can supports several different stereo graphics options.
Stereo figures are often used in molecular graphics illustrations in order to provide the reader with a three-dimensional view using a two-dimensional sheet of paper. To achieve a satisfying 3D effect, care must be taken to insure that the stereo pairs are generated with the proper transformation and printed with the correct separation between images.
A key challenge in preparation of stereo figures is the fact that journals usually shrink images before they are printed. In preparing your figure, it is essential that your drafts correspond to the final printed size. You may need to obtain this information from the journal ahead of time.