VMD User's Guide

6. The Stereo chooser changes the stereo mode, while the Eye Sep and Focal Length controlschange the eye separation distance and the focal length, respectively.• Cachemode –TheCachemode toggle controls whether or not VMD uses a display list cachingmechanism to accelerate rendering of static geometry. This feature can be extremely beneficialfor achieving good interactive display performance on tiled display walls, and for remotedisplay over a network. Caching cannot be performed while animating trajectories, so theperformance benefit is only possible interactive rotation and zooming of static molecularstructures.• Rendermode –TheRendermode chooser controls which low-level rendering method VMDuses. The Normal rendering mode is the default VMD rendering algorithm based on standardfixed-function OpenGL. The AlphaBlend rendering mode is an alternate implementationwhich requires the Sun Global Alpha OpenGL extension. This feature allows VMD to usea high quality alpha-blended transparency mode with no performance loss compared to thescreen-door method it normally uses. On machines lacking the Sun Global Alpha extension,this rendering mode will not be available. The GLSL rendering mode uses OpenGL ProgrammableShading Language to implement real-time ray tracing of spheres, alpha-blendedtransparency, and high-quality per-pixel lighting for all geometry. On machines with highperformance graphics boards supporting programmable shading, the GLSL rendering modeprovides quality on par with many of the external software renderers supported by VMD butat interactive display rates.• Clipping Planes (Near Clip and Far Clip) – These controls are found in the DisplaySettings form. Only those parts of the scene between the near and far clipping planes aredrawn. The display clipping planes also set the depth cueing start and endpoints. Objects atthe near clipping plane are distinct and crisp, objects at the far clipping plane will be blendedinto the background. Clipping planes positions are changed with the Near Clip and Far Clipcontrols. It is not possible for the near clip to be farther away than the far clip. When usingstereo, it may be useful to set the near clip plane much lower than the default value. Thismakes the geometry “pop out of the screen” a bit more, and can be used for greater dramaticeffect.• Screen Height (Hgt) and Distance (Dist) – These controls are found in the DisplaySettings form. The screen height, along with the screen distance, defines the geometry andposition of the display screen relative to the viewer. The screen height is the vertical size ofthe display screen, in ‘world’ coordinates. Each molecule is initially scaled and translated tofit within a 2 x 2 x 2 box centered at the origin; so the screen height helps determine howlarge the molecule appears initially to the viewer.The screen distance parameter determines the distance, in ‘world’ coordinates, from the originto the display screen. If this is zero, the origin of the coordinate system in which molecules(and all other graphical objects) are drawn coincides with the center of the display. If distanceis negative the origin is located between the viewer and the screen, if it is positive, the screenis closer to the viewer than the origin. A negative value puts any stereo image in front of thescreen, aiding the three-dimensional effect; a positive value results in a stereo image that isbehind the screen, a less dramatic effect (but easier to see, for some people) stereo effect.Figure 4.5 describes the relationship between the screen height, the screen distance, and theworld coordinate space.38