VMD User's Guide

sci-fi and horror movie showings. The computer hardware requirements for Anaglyph stereo arecurrently the same as for CrystalEyes stereo except that LCD shutter glasses and emitters are notrequired. The red-blue glasses take the place of the LCD shutter glasses used for the CrystalEyesstereo modes. Anaglyph stereo has one major disadvantage when compared with CrystalEyesstereo, which is that its color rendition is obviously severely constrained. This is just a fact of lifewith Anaglyph stereo, and it is up to the user to use color schemes for their molecules that stilllook visually pleasing when displayed in Anaglyph stereo mode.6.3.5 CrystalEyes StereoCrystalEyes stereo is the name used within VMD for the quad-buffered frame-sequential stereodisplay mode found on appropriately equipped graphics workstations. Typically this mode is usedto drive LCD shutter glasses with a CRT display or projection system.Quad-buffered frame-sequential stereo is available on workstations such as SGI InfiniteReality,Sun XVR-1000, XVR-4000, HP SV6, NVidia Quadro FX, and others. This mode provides separateleft and right eye frame buffers. It allows the a window display in stereo, while all other windowsappear as normal. Quad-buffered stereo modes usually display at lower-resolution since they requiretwice as much video memory as non-stereo display modes. The display must be set in a stereocapablemode before starting VMD. On SGI systems, one must use either the setmon or xscreenutilities to configure the display mode. On Sun systems this is done using the fbconfig utility.HP systems use the sam utility for display configuration. Windows machines use the DisplayProperties tab to control video board display mode settings.Once set in the proper display mode, start VMD as normal, and select ‘CrystalEyes stereo’from the Display form. The image should switch to two images nearly superimposed, but slightlyoffset.6.3.6 Stereo ParametersA stereo image is generated by drawing two images from two different perspectives, one from theleft eye and one from the right. The images are made by finding the view that would be seenby someone located inside the scene. The method uses two parameters to find the view; the eyeseparation and the focal length. The first defines the distance between the eyes and gives theparallax effect. Setting the separation to 0 will result in a flat 2D image, while setting it too largewill give most people a headache.The graphics model used by VMD assumes the eyes looking in front of the viewer and focusingat the same point the focal length away. If the focal length is 0, the viewer’s eyes are crossed andlooking at each other. A larger focal length will often help in creating a viewable image.The two parameters can be changed with the text commands display focallength anddisplay eyesep, orusingtheDisplay form [§4.4.6].In general, try to make the eye separation as large as possible without giving the viewer amigrane, and try to vary the focal length to cut down on double images. It may often help totranslate the molecule forward or backward and also adjust the scaling, since there is typically anoptimum position for a molecule for a given set of stereo parameters.83