Chapter 4: Viewing the Workspace
Maestro 10.2 User Manual
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zoom in and out in the Workspace. If you deselect this option, the top view stays the
same, regardless of what happens in the Workspace. Translation in x and z moves the dis-
played structures.
• Clipping planes: These are horizontal lines that mark the planes where the graphical
image is clipped. The lower line marks the plane that is closest to the viewer, and the
upper line marks the plane furthest from the viewer.
The planes can be moved by dragging the horizontal lines. To move both planes in the
same direction, hold down the
CTRL
key and drag one of the planes or use the scroll
wheel. To move both planes in opposite directions, hold down the
SHIFT
key and drag
one of the planes or use the scroll wheel. You can use the keyboard to move the planes
closer together (
F
), further apart (
G
), towards you (
=
), or away from you (
-
), in small
increments. These actions are also available from
View
→
Move Clipping Planes
.
The clipping planes are adjusted if you select
Adjust clipping planes when focusing on a
substructure
under
Workspace
→
Clipping Planes
in the
Preferences
panel (see
Section 14.4.8 on page 351
) and you do one of the following:
• Select part of a structure and perform a fit-to-Workspace.
• Perform a fit-to-ligand.
• Middle-click a residue in the sequence viewer to zoom in on it.
• Select a residue in the residues table of the
Density Fit
panel (PrimeX)
• Select a rotamer in the
Residues
table of the
Rotamers
dialog box.
• Find a residue with the
Find
toolbar.
• Viewing volume indicator: This is a green box that represents the viewing volume. As
you zoom in on the structure, the box shrinks. If you have perspective enabled, the view-
ing volume box is trapezoidal, with the small side at the bottom.
Clipping can be applied to fit objects in the Workspace, by choosing
To All Atoms
,
To Selected
Atoms
, or
To Ligand
from the
Move Clipping Planes
submenu of the
View
menu. This feature
can be used to reset the clipping without changing the zoom.
Clipping can be applied selectively, as well as to all graphical objects. To choose what clipping
is applied to, right-click in the clipping planes window and make your choice from the shortcut
menu that is displayed. The choices are:
•
All
—Apply clipping to all objects (structures and surfaces). Clipping planes are drawn as
horizontal orange lines, and can be adjusted by dragging.
•
Surfaces
—Apply clipping to surfaces but not to structures. There are four clipping
planes: front, back, left, and right. These planes are drawn as horizontal and vertical pur-
ple lines, and can be adjusted by dragging.
Chapter 4: Viewing the Workspace
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•
Surfaces to selected atoms
—Apply clipping to the surfaces using a cube centered on the
selected atoms. For example, you might select just the ligand in a ligand-receptor com-
plex, and the surface will be clipped to a cube that contains the ligand. The outline of the
cube is displayed in cyan. You can resize the cube by dragging horizontally.
•
Selected atoms
—Apply clipping only to the selected atoms. For example, you could
select the receptor in a complex, and leave the ligand unclipped. Clipping planes are
drawn as horizontal cyan lines, and can be adjusted by dragging.
4.7
3D Viewing
Maestro provides several tools to enhance the 3D appearance of complex structures. These
tools include stereo viewing, perspective, fogging distant atoms, and depth cues. They are
described in the sections that follow. Most of the tools are in the
3D
and
Fog
tabs of the
Appearance
panel, which you can open by choosing
View
→
3D Options
or
View
→
Fog
→
Settings
.
4.7.1
Stereo Viewing
Maestro provides two kinds of stereo viewing method: software stereo and hardware stereo.
Software stereo can be run on any computer, and can be run across a network or with remote
display software, such as NX or Remote Desktop. It usually involves displaying both images
on the screen simultaneously, and relies on focusing or simple devices to view the stereo effect.
Hardware stereo requires some special equipment—a specialized monitor or graphics card, or
both, and 3D glasses. It can usually only be viewed locally.
Two software stereo methods are available. In the first, two images are displayed simultane-
ously on separate parts of the screen, and the stereo effect relies on focusing your eyes so that
the images appear to merge into a single image. Two variants of this method are available:
“wall-eyed”, in which the left eye looks at the left image and the right eye looks at the right
image (focusing at a very long distance); and cross-eyed, in which the left eye looks at the right
image and the right eye looks at the left image (focusing at a very short distance). Neither of
these variants needs any special hardware, though a device for screening out one image for
each eye may be useful. The default variant is wall-eyed.
The second software stereo method is anaglyph stereo, in which the images are superimposed
and are drawn with color filters, red and blue-green. To view the stereo effect, you need a pair
of glasses with the appropriate color filter for each eye. The images have full color, but the red
colors are not as true as when you do not view in stereo.