Instead, we suggest making one image of the current scene, then shift the molecules to the left (or right) to make the other image. (Note that neither the stage nor the axes will move, so they will not be in stereo.) The text commands for this are something like:
render Raster3D left.r3d trans by -.1 0 0 render Raster3D right.r3d
The two files must then be rendered to produce the rgb file. As it turns out, this method makes it easy to produce stereo images of ordinary Raster3D files. Since VMD can read the Raster3D format, all you have to do is read the file and then execute the commands listed above. The text commands for generating left or right views also have equivalents in the GUI under the Stereo option of the Display form.