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Appearance Panel |
The Appearance panel is used to change display settings such as background color, lighting and materials effects, and 3D effects, including stereo.
To open the Appearance panel, you can:
Choose Workspace → Appearance in the main window.
The background color can be set by clicking the color button and choosing a color in the standard color selector that opens, or by clicking one of the five preset color buttons. The color change takes effect immediately.
Background color can also be set using text commands. An example follows.
Command Syntax: displayopt [bgcolor=colorname |
bgcindex=colorindx]
Examples:
To color background red: displayopt bgcolor=red
To color background with the color at color index 5: displayopt bgcindex=5
The lighting tab contains controls for the lighting effects on objects in the Workspace.
The light direction control allow you to pick the direction of the selected light. To change the direction, click the desired location on the red ball, or drag the yellow spot to the desired location.
Select the light source for which the direction and properties are to be adjusted.
Select this option to use the selected light. Deselecting this option disables the controls for the light.
Set the ambient value with the slider, or enter the value in the text box. This is the relative intensity of the (ambient) nondirectional light.
Set the diffuse value with the slider, or enter the value in the text box. This is the relative intensity of diffuse reflection (reflection that has the same intensity in all directions).
Set the specular value with the slider, or enter the value in the text box. This is the specular reflection intensity ("shiny" reflection of the light source)
Restore the settings to their default values.
The materials tab contains controls for the definition of the appearance of the objects in the Workspace. Some preset material and lighting styles are available on the Style toolbar.
Select the object whose material appearance is to be customized.
These four buttons, Metallic, Plastic, Rubber, Wood, set values of the properties that control the appearance of the selected object.
This section allows you to set the five properties of the material:
Each property has a slider and a text box. You can use either of these controls to set the property value.
The Minimize performance cost option disables the Ambient and Diffuse controls, and uses these properties to track color. This option is only present when the OpenGL level is 1.2.
The Environment map option menu provides a selection of environments that are shown as reflections on the surfaces of the objects in the Workspace. This menu is only present when the OpenGL level is 2.1.
Restore the settings to their default values.
The 3D tab contains the Stereo tab and the Perspective tab. The common controls, located below the tabs, are described first, then the tabs themselves.
This slider translates the region of molecule space bounded by the front and back clipping planes. This appears to move objects within that region, in or out (along the z-axis), relative to the screen. Smaller alignment depth values place the displayed objects farther from the viewer (farther behind screen). Larger values place objects closer to the viewer (farther in front of screen).
This option determines whether the front and back clipping planes should be automatically adjusted to preserve the eye separation while displaying in stereo and to preserve the perspective scale (corresponding to viewing distance) when displaying in perspective. When this option is enabled, perceived depth is maintained but some objects may be clipped, especially when zooming in (in which case, you may also want to adjust the alignment depth). If Adjust clipping to preserve depth cues is deselected, then the stereo and perspective settings are automatically adjusted in order to preserve the front and back clipping planes. Then, objects are not clipped more in front and back when zooming in, but are effectively flattened (reducing their perceived depth). These automatic adjustments are not permanent, but are done whenever the current 3D settings cannot be used to display, in an acceptable manner, the entire region between the front and back clipping planes.
Click this button to move the front and back clipping planes in to the fit the parts of the structure currently displayed in the Workspace. This helps the stereo and perspective depth cues work more effectively for the spatial region of interest, reducing the need to clip objects or sacrifice depth cues in order to accommodate the display of unoccupied regions of space.
You can also choose View → Fog → Enhance Depth Cues.
The settings in the Stereo tab allow you to view the structures displayed in the Workspace in stereo and to switch between the stereo viewing methods. Stereo display only applies to the Workspace—none of the Maestro main panel tools or other panels are displayed in stereo. You might want to use full-screen mode when you are viewing structures in stereo, which you can turn on and off with Ctrl+= (⌘=), or by choosing Workspace → Full Screen and using ESC to exit.
You can also adjust the alignment depth to shift objects that you want to see more clearly in stereo toward the plane of the screen.
The stereo method and settings persist across Maestro sessions.
Turn on the use of stereo display. This can also be done in the main window with Ctrl+S (⌘S) or by choosing View → Stereo.
Select this option to swap the images for the right eye and the left eye. This is useful to resolve synchronization problems with hardware stereo. It applies also to the software stereo methods, and has the effect of swapping cross-eyed and wall-eyed stereo.
Select a stereo viewing method from this option menu. There are five stereo viewing options, three of which are software implementations and do not require special hardware, and the other two are hardware stereo methods. The software methods can be used on any computer, and displayed remotely. The hardware methods can usually only be used locally.
Wall-eyed— In the "wall-eyed" stereo viewing method, the eyes focus on both displayed images at once, instead of focusing at a central point. One difficulty that may arise when using this stereo viewing method is that it is difficult, if not impossible, to achieve the stereo effect when the images are more than the inter-ocular distance apart, or about 2.5 inches. Structures more than 2.5 inches wide will therefore need to be resized and repositioned using the Size factor and Separation factor sliders. The height of the molecule is not critical for stereo viewing. Any height less than the window height is acceptable.
To use the Wall-Eyed stereo viewing option, stare past the screen as if focusing on an image far beyond it. This tactic tricks the eyes into focusing in a plane beyond the screen. When performed correctly, wall-eyed viewing produces three images, with the center one being a 3D combination of the two outer ones.
Cross-Eyed—This stereo method is difficult and is not advised for stereo viewing novices, since inadvertently viewing the cross-eyed image wall-eyed will result in the molecule being inverted along the z-axis. This can produce inaccurate depth information, particularly when the wire molecular representation is being used.
Hardware—Technically, this is quad-buffered hardware stereo. It requires a suitable monitor, with a refresh rate greater than 100 Hz, a graphics card that supports quad-buffered stereo, and 3D glasses. A warning is displayed if the hardware does not support stereo and this option is selected. This option is not available on Mac platforms, which do not in general support hardware stereo.
There are other specialized viewing devices that can be used with this method.
Interlaced—This hardware method requires a monitor that supports interlacing, and 3D glasses. Interlaced stereo works on all supported platforms if the hardware is available. A warning is displayed if the hardware does not support stereo and this option is selected.
Anaglyph—This stereo method uses color filters to display the two images. To use it, you must have glasses with one red and one cyan filter. The stereo image is perceived in full color, though the red colors tend to be somewhat dull.
Use this slider to reduce the size of the displayed structure to better facilitate cross-eyed or wall-eyed viewing.
Use this slider to decrease the distance between the left and right stereo images. This feature eases cross-eyed and wall-eyed viewing. The Separation factor slider becomes available once the displayed structures have been resized with the Size factor slider (see above).
Use this slider to adjust the stereo viewing angle, which governs the amount of depth perceived in stereo. The stereo viewing angle increases roughly in proportion to eye separation, and increases with perspective scale (decreases in nearly inverse proportion to viewing distance). The slider should generally be positioned near the center of the range, to correspond to a "normal" adult inter-ocular distance of 2.5 inches and viewing distance of 24 inches. Use smaller values for smaller inter-ocular distance or larger viewing distance, or to reduce the side-effects of larger stereo angles, such as clipping and double images. Use larger values for larger inter-ocular distance or smaller viewing distance, or to increase the amount of perceived depth.
Reducing this parameter can help stereo perception with interlaced stereo on certain monitors.
The Perspective feature helps facilitate 3D viewing by scaling the apparent size of objects according to their z-axis depth (making more distant objects appear smaller, as in normal viewing). To use perspective, select Display in perspective. Perspective is enabled by default.
The amount of perspective, which relates to the viewing distance, can be
adjusted using the Perspective scale slider.
Here, perspective scale is the ratio between the actual size and the
projected size of an object placed 0.7 feet behind the display screen.
This has a corresponding viewing distance,
view_dist = (0.7 ft) / (perspective_scale - 1)
For a known viewing distance,
perspective_scale = 1 + (0.7 ft / view_dist)
Therefore, for a normal viewing distance of 2 feet,
perspective_scale = 1 + (0.7 ft / 2 ft) = 1.35
To get a stronger depth cue, using exaggerated perspective, you can use
larger perspective scale values.
The Alignment depth slider can be used to shift objects in or out of the screen, in order to change their relative size (depth scaling) or clipping.
When perspective is in use, the viewing volume indicator (shown in green in the clipping planes window) takes a trapezoidal shape that reflects the perspective scale.
The Fog feature helps facilitate 3D viewing by providing emphasis on the parts of the structure that are closest to you. Closer parts of the molecule appear in the pure currently selected atom color, and more distant parts appear to turn gray and finally disappear into the background. Fog can be useful when hardware-assisted stereo viewing is not available, but it is also helpful when used in conjunction with stereo viewing.
Select the conditions under which fogging is used.
The use of fogging can be controlled from the
View → Fog menu in the main window.
You can also do this with the Fog button menu on the
View toolbar in the main window.
Apply fogging to atom labels as well as to atoms.
This option menu contains three fogging gradient types: Linear, Exponential, and Exponential Squared. Currently, only the Linear method should be used when displaying in perspective.
The Linear Start and Linear End sliders allow you to increase or decrease the range of available colors created by fog gradations. Linear Start moves the plane that defines the fog boundary that is closest to the screen. Linear End moves the fog boundary that is behind the structure. There is a finite number of gradations, and if there is empty space, some of them are wasted.
This slider allows you to increase the contrast of colors created by the fogging feature. Closer portions of the structure will appear even brighter and more distant ones will more quickly converge on the background color.
This tab allows you to apply special effects to the Workspace. The effects are calculated for the full screen for each pixel. The effects can be turned on and off using the checkboxes. The available effects are as follows:
Antialiasing—smooth the edges of objects so they don't appear jagged. This effect does not antialias semi-transparent objects. The Full-scene antialiasing preference (under Workspace – Graphics) does, but it does not antialias spheres and cylinders (balls and sticks). For the smoothest edges, use both the preference and the screen effect.
Ambient occlusion—enhance the perception of depth by taking into account the ambient lighting blocked by other objects. The Enhanced depth view preference (under Workspace – Depth view) uses ambient occlusion based on atoms, and is only available for structures in CPK representation. This option is available for any structure, but is most useful for large structures in CPK representation and with molecular surfaces.
You can set the intensity of the darkening effect with the Intensity slider and box. The intensity is represented as a percentage, with 0 corresponding to no effect.
You can also change the range of the effect, with the Radius slider. Any screen object within the specified radius of a pixel is considered to occlude the pixel. Thus, the smaller the radius, the more local and "sharp" the effect, At a very small radius, the effect is like outlines.
Outlines—Add a thin outline to objects in the Workspace. The color of the outline can be set by clicking the Color button and choosing a color in the color selector that opens. The new color is shown on the color button. The width of the outline in pixels can be changed in the Width box, from 0 to 10.
Cartoon shading—Use cartoon shading, in which the color or shading is done in steps rather than continuously. You can specify the number of steps in the Steps box, which can take values from 2 to 10.
This tab is not present if the OpenGL level is 1.2, as it requires features that are not present at this OpenGL level.
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