Maestro User Manual

Chapter 4: Viewing the Workspace

Maestro 10.2 User Manual

75

Figure 4.3. The Stereo tab in the Appearance panel.

For hardware stereo, Maestro supports both quad-buffered hardware stereo and horizontally

interlaced stereo. Details of the hardware and software requirements can be found in the 

Instal-

lation Guide

. 

In quad-buffered stereo, the left and right images are displayed alternately on the screen. To

reduce flickering, a monitor with a sufficiently high refresh rate is needed (better than 100 Hz). 

In horizontally interlaced stereo, the left and right images are displayed on consecutive lines on

the screen. The resolution is therefore not as high as for quad-buffered stereo, and text can be

difficult to read. If the interlacing also alternates between left and right images each time the

screen is refreshed (field-sequential interlacing), the synchronization with the glasses may be

inverted. This can be fixed as described below.

To set the stereo viewing options, choose 

View 

→

 3D Options

 in the main window and select

the 

Stereo

 tab. To select a stereo viewing method, choose 

Wall-eyed

, 

Cross-eyed

, 

Interlaced

, or

Hardware

 from the 

Method

 option menu. To view the Workspace in stereo, select 

Display in

stereo

 in the panel, or choose 

View 

→

 Stereo

 or press 

CTRL+S

 in the main window. These

actions also turn off stereo viewing.

If you are using hardware stereo and the synchronization is inverted, select 

Swap stereo

images

. (This option also swaps cross-eyed and wall-eyed software stereo.)

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Chapter 4: Viewing the Workspace

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If you are using the cross-eyed or wall-eyed method and the displayed stereo pairs are more

than 2.5 inches from each other, adjust the 

Size factor

, 

Separation factor

, and 

Eye separation

controls to bring the structures closer. This will make stereo viewing easier.

With any stereo method, you can adjust the eye separation and the alignment depth. Adjusting

the eye separation changes the amount that the stereo image appears to extend into and out of

the screen—the stereo depth—and adjusting the alignment depth makes the stereo image

appear to move into or out of the screen. Decreasing the eye separation factor can help for

interlaced stereo on some monitors. 

The stereo method and stereo settings (size and separation) persist across Maestro sessions:

they are saved in prefer.cmd in your profile directory. 

4.7.2

Using Perspective

The 

Perspective

 feature enhances 3D graphical representation by scaling objects in the Work-

space in proportion to their distance from the viewing plane (“camera”). Perspective is enabled

by default. You can turn it on and off by choosing 

View 

→

 Perspective

.

Figure 4.4. The Perspective tab in the Appearance panel.

The perspective controls are in the 

Perspective

 subtab of the 

3D

 tab. You can adjust the scaling

using the 

Perspective scale

 slider. A larger value gives a stronger impression of depth (“depth

cue”). The green lines in the Clipping Planes window move to reflect the viewing volume

available at a given value on the 

Perspective scale

.

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Chapter 4: Viewing the Workspace

Maestro 10.2 User Manual

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4.7.3

Using Fogging

The 

Fog

 feature changes atom colors in the displayed structure so that they fade toward that of

the background as atom coordinates grow increasingly negative in the z direction. This feature

is particularly useful for depth-cueing when viewing large structures, such as proteins, and

when using the 

Wire

 molecular representation. 

Figure 4.5. The Fog tab in the Appearance panel.

The fog controls are in the 

Fog

 tab of the 

Appearance 

panel. To enable fogging, select 

On

 or

Automatic

 from the 

Display fog

 option menu. You can independently apply fogging to atom

labels using the 

Display fog on atom labels

 option. You can also turn fogging on or off from the

Fog

 submenu of the 

View

 menu or from the 

Fog 

button menu on the 

Workspace

 toolbar.

Automatic fogging means that fogging is turned on when a molecule is bigger than a given

number of atoms. Below this threshold, fogging is turned off. The threshold is 40 atoms, and

can be set with the Maestro command displayopt fogcutoff=number. 

The default method for fogging employs linear fall-off for the brightness of the displayed

structural elements. To exaggerate the fogging effect, you can select either the 

Exponential

method or 

Exponential squared

 method. When you are displaying a structure in perspective,

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