PyMOL does work with the NVidia 3D NVision setup, but needs the right hardware. For example, PyMOL does work with a FX 580. Please see the following links for more help on setting up the 3D NVision System on your machine with a Quadro card.
Please note that the Quadro FX1400 does not support stereographic viewing in Win7. The response from NVidia is: most stereo features on Windows 7 are only support[ed] on Quadro *600 series(G80) and beyond. I believe clone mode stereo is support on Quadro *500 series(G70) and beyond.
If you build PyMOL from the open-source code and want to use it with an iZ3D, use these instructions:
If you are using incentive PyMOL, use these instructions;
Zalman monitors use interlaced technology to create the 3D effect. All odd numbered lines go to the right eye (for example) and all even numbered lines can go to the left eye. This creates two separate images for the viewer, thus creating the 3D effect.
This solution is cheaper than the NVidia NVision systems as all you need is a Zalman monitor (no Quadro card or 3D NVision kit necessary). However, the Zalman 3D does have limitations: