My guess is that the problem you are having is that the focal plane, basically where the molecule intersects the screen, is too far back, so when parts of the molecule are far out of the screen, your eyes are having problems converging, and you're getting an inversion. To test this hypothesis, bring up the SideView tool, and switch to the "top" side view from the "right" side view. You will then see a dashed line that represents the focal plane. Drag the focal plane all the way to the near plane (the solid vertical line closest to the eye), and then try your rotating experiment again. And please let me know if that is really the problem you're having. Automatically managing the focal plane in stereo is something chimera needs to do, and there is experimental support for that if you run the following Python code (either in the IDLE window, or place it in a .py file and open the python file within chimera): chimera.viewer.camera.autoFocus = True But not all parts of chimera respect that setting, so it is still possible for the focal plane to get out of whack and you'll need to adjust it by hand. HTH, Greg On 08/29/2011 10:50 AM, frederick lee wrote:
dear chimera community, i have experienced this issue for some time now. i don't think this is happening with other software like pymol, dsvisualizer, MOE, etc given the same computer and hardware setup.
somehow when viewing in hardware stereo mode (sequential stereo), the model will switch back and forth between proximal and distal views during rotations. is there a particular chimera setting that will prevent such from happening. thanks much. fred