Molecules may be rendered in stereo, which can greatly enhance the appearance and visual content of the displayed systems. There are several stereo formats available:
Side-by-side stereo means that the normal display is divided into two halves, a left view and right view, each occupying one-half of the original display area. Each view displays the current molecules from a slightly different perspective, corresponding to the left and right eye of the viewer. The images are separated, however, so to actually see a 3D object you must direct your eyes until the two images are on top of each other, and then focus on the resulting image until you can see it as three-dimensional.
There are two ways of placing the images. In wall-eyed stereo, the left eye's image is located on the left side of the display, and the right eye's image is on the right. This is the standard method for displaying stereo images in publications as it works well when the display (in this case, the piece of paper) is close to the eyes. It is called wall-eyed because your eyes are directed the same way they would be if looking at a distant wall.
In cross-eyed stereo, the left eye's image is located on the right side of the display, and the right eye's image is on the left, and hence the name cross-eyed. This is mostly used for distant displays (such as overhead projections) as it is much easier to cross eyes at that range than use the wall-eyed method -- you are already looking at the wall.
Crystal Eyes stereo refers to a special hardware option available on Silicon Graphics workstations that allows one to view three-dimensional objects through the use of a special display monitor mode and special stereo viewing glasses. Stereographics Corp. is one such supplier of these glasses. This mode also requires special infrared emitters to synchronize the stereo glasses with the display monitor.
There are at present two types of Crystal Eyes stereo modes available on SGI machines; which one used depends on the available graphics hardware (see the man page stereo(7)). Follow the outline below for the relevant graphics option:
This will change the display characteristics to the lower resolution mode, with a higher display frequency (108 Hz), but will not change the managed size of the X-Window display screen. To change back to the normal mode (after running VMD ), execute the command:
/usr/gfx/setmon -n 1280x1024_60
When the computer is in the lower resolution mode, run VMD as normal, but note that the lower resolution means the windows will appear larger and may end up sometimes positioned off-screen. If this is a problem, a system superuser should set the video mode permanently with the commands listed in the next item.
/usr/gfx/setmon -x 960x680_108s; /usr/gfx/stopgfx; /usr/gfx/startgfx &
To reset the computer to regular 1280x1024 use, execute the command: /usr/gfx/setmon -x 1280x1024_60; /usr/gfx/stopgfx; /usr/gfx/startgfx &
It may be useful, if stereo-in-a-window will be used often, to set the monitor to the lower resolution mode, and leave it that way.
Once set in the proper display mode, start VMD as normal, and select `Crystal Eyes stereo' from the display window pop-up menu. The image should switch to two images nearly superimposed, but slightly offset.
There have been problems with crystal eye stereo in recent Indigo machines. These appear to have been fixed with the following IRIX patches, available from SGI:
??? list stereo patches here ??
A stereo image is generated by drawing two images from two different perspectives, one from the left eye and one from the right. The images are made by finding the view that would be seen by someone located inside the scene. The method uses two parameters to find the view; the eye seperation and the focal length. The first defines the distance between the eyes and gives the parallax effect. Setting the seperation to 0 will result in a flat, 2D image, while setting it too large will give most people a headache.
The graphics model used by VMD assumes the eyes looking in front of the viewer and focusing at the same point the focal length away. If the focal length is 0, the viewer's eyes are crossed and looking 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 and display eyesep, or using the Display form.
In general, try to make the eye separation as large as possible without giving the viewer a migrane, and try to vary the focal length to cut down on double images. It may often help to translate the molecule forward or backward and also adjust the scaling, since there is typically an optimum position for a molecule for a given set of stereo parameters.