Display Menu and Display Settings Window

Figure 5.4: The Display menu

The Display menu controls many of the characteristics of the graphics display window. The characteristics which may be modified include:

• Reset View - This menu item can be used to force VMD to reset the scene back to the default viewing orientation and scale as is done when a molecule is first loaded.

• Stop Rotation - This menu item stops autorotation of the scene. The scene can be autorotated by quickly dragging the mouse while briefly depressing and releaseing the mouse button, leaving the scene spinning until it is stopped either by this menu item or by further mouse interactions.

• Perspective - The view of the scene can be Perspective or Orthographic. In the perspective view (the default), objects which are far away are smaller than those near by. In the orthographic view, both objects appear at the same scale. Note that several of the supported external rendering programs do not support orthographic rendering. As such, it may be necessary to ``fake it'' by translating the scene far away from the camera, and apply a zoom factor. This has the effect of significantly reducing the perspective, while not truly an orthographic view.

• Antialiasing - Turns antialiasing on or off. Antialiasing helps smooth out the jagged appearance of displayed geometry resulting from the inherently discrete pixels on the display device. The antialiasing feature is only available on platforms which support full-screen antialiasing, sometimes known as ``multisample antialiasing''. On platforms lacking the multisample capability, there may be alternate ways to perform full-screen antialiasing by selecting an option in the display driver setup. Windows machines most commonly place these controls in the display driver configuration panel.

• Depth Cueing - Turns depth cueing on or off. Depth cueing causes distant objects to blend into the background color, in order to aid in 3-D depth perception. The depth cueing settings controlled in the Display Settings window. The Cue Mode parameter controls which type of fog equation is used. The Linear depth cueing mode provides a simple depth gradient with a defined starting point and endpoint. The Exp and Exp2 depth cueing modes take a density parameter, and generally blend into the background color much more sharply than the linear depth cueing mode. Scaling up the molecule will increase the amount of depth cueing effect that is visible, since it will occupy a larger depth range. Scaling the molecule size down decreases the depth cueing effect. Translating the molecule into and out of the screen will cause it to blend into and out of the background color.

• Culling - Turns backface culling on or off. This feature is primarily used to accelerate rendering performance on software based implementations of OpenGL, such as Mesa. Backface culling actually reduces performance on some hardware renderers, so you'll have to use your own best judgement on whether or not it is helpful to use on your specific computer system.

• FPS - This option enables or disables on-the-fly display of the achieved VMD rendering frame rate. The frame rate is displayed in the upper right hand corner of the graphics window when it is enabled.

• Lights - The graphics display window can use up to four separate light sources to add a realistic effect to displayed graphical objects. The Lights On browser turns these light sources on or off. If the number is highlighted, the light is on, and clicking on it turns the light off. See section 5.1.1 for more discussion regarding lights.

• Axes - A set of XYZ axes may be displayed at any one of five places on the screen (each of the corners or the center) or turned off. This is controlled by the Axes chooser.

• Background - The display background can either be set to a uniform color over the entire scene, or a vertical gradient can be set with a linearly changing color from the top of the viewport to the bottom.

• Stage - The Stage browser controls the stage, which is a checkerboard plane that can be located in any one of six places or turned off.

• Stereo, Eye Sep, and Focal Length - These controls are found in the Display Settings window. These controls set the stereo mode and parameters; stereo is discussed fully in chapter 7. The Stereo chooser changes the stereo mode, while the Eye Sep and Focal Length controls change the eye separation distance and the focal length, respectively. The Stereo Eye Swap control optionally reverses the left/right eyes when displaying on projectors or other devices that for one reason or another don't preserve the correct left/right eye assignments.

• Cachemode - The Cachemode toggle controls whether or not VMD uses a display list caching mechanism to accelerate rendering of static geometry. This feature can be extremely beneficial for achieving good interactive display performance on tiled display walls, and for remote display over a network. Caching cannot be performed while animating trajectories, so the performance benefit is only possible interactive rotation and zooming of static molecular structures.

• Rendermode - The Rendermode chooser controls which low-level rendering method VMD uses. The Normal rendering mode is the default VMD rendering algorithm based on standard fixed-function OpenGL. The GLSL rendering mode uses OpenGL Programmable Shading Language to implement real-time ray tracing of spheres, alpha-blended transparency, and high-quality per-pixel lighting for all geometry. On machines with high performance graphics boards supporting programmable shading, the GLSL rendering mode provides quality on par with many of the external software renderers supported by VMD but at interactive display rates.

• Clipping Planes (Near Clip and Far Clip) - These controls are found in the Display Settings window. Only those parts of the scene between the near and far clipping planes are drawn. The display clipping planes also set the depth cueing start and endpoints. Objects at the near clipping plane are distinct and crisp, objects at the far clipping plane will be blended into the background. Clipping planes positions are changed with the Near Clip and Far Clip controls. It is not possible for the near clip to be farther away than the far clip. When using stereo, it may be useful to set the near clip plane much lower than the default value. This makes the geometry ``pop out of the screen'' a bit more, and can be used for greater dramatic effect.

• Screen Height (Hgt) and Distance (Dist) - These controls are found in the Display Settings window. The screen height, along with the screen distance, defines the geometry and position of the display screen relative to the viewer. The screen height is the vertical size of the display screen, in `world' coordinates. Each molecule is initially scaled and translated to fit within a 2 x 2 x 2 box centered at the origin; so the screen height helps determine how large the molecule appears initially to the viewer.

  The screen distance parameter determines the distance, in `world' coordinates, from the origin to 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 distance is negative the origin is located between the viewer and the screen, if it is positive, the screen is closer to the viewer than the origin. A negative value puts any stereo image in front of the screen, aiding the three-dimensional effect; a positive value results in a stereo image that is behind the screen, a less dramatic effect (but easier to see, for some people) stereo effect.

  Figure 5.5: Relationship between screen height (SCRHEIGHT), screen distance to origin (SCRDIST), and the viewer

  

  Figure 5.5 describes the relationship between the screen height, the screen distance, and the world coordinate space.

• Shadows - The shadows control enables and disables direct lighting shadowing when using the built-in Tachyon CPU or GPU renderers or when exporting the VMD molecular scene to external renderers that implement shadowing algorithms. The simple direct lighting model implemented in most renderers yields shadows that are completely dark, producing a somewhat harsh lighting quality akin to what would be expected in a desert under full sunlight with no clouds.

• Ambient Occlusion - The ambient occlusion (AO) lighting control enables the use of so-called ambient occlusion indirect lighting when using the built-in Tachyon CPU or GPU renderers, or external renderers that implement AO. Images with much higher quality shading can be produced by augmenting direct lighting with ambient occlusion or broad angle or indirect lighting techniques. Ambient occlusion lighting emulates the broad lighting effects similar to what would be experienced on a cloudy or overcast day with omnidirectional light arriving on all surfaces. The AO ambient coefficient controls the strength of the omnidirectional lighting components. The AO direct coefficient scales the direct lighting contribution associated with the directional and positional lights.

• Depth of Field (DoF) - The depth of field (DoF) control enables or disables emulation of depth of field focal blur effects associated with fast focal ratio camera optics and close focus distances. The depth of field implementation provided by the built-in Tachyon ray tracer and most other renderers yields a plane of perfect focus at a specified distance from the camera. The degree of focal blurring with increasing distance from the plane of perfect focus depends on both the simulated f/stop and the distance between the plane of perfect focus and the camera.