Stereo_mode sets how PyMOL displays the screen for the array of available stereo 3D options. A few of the available stereo_mode settings are:
set stereo_mode, 2 # cross-eye stereo set stereo_mode, 3 # wall-eye stereo set stereo_mode, 10 # red-cyan (i.e. movie theatre 3-D glasses) stereo
Changing the orthoscopic view setting may also be helpful when trying to view in 3D.