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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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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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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,