Chapter 4: Viewing the Workspace
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you should use linear fall-off. The
Automatic
method uses linear fall-off with the start and end
points determined by the background color.
The points at which fogging begins and ends can be controlled with the
Linear start
and
Linear
end
sliders. Adjusting
Linear start
moves the boundary at which fogging starts between the
front (0.0) and the back (1.0) of the displayed structure. Adjusting
Linear end
moves the fog
boundary that is behind the structure further back, to a maximum of twice the depth of the
displayed portion of the structure. By adjusting these boundaries you can control the amount
by which the structure appears to fade into the background.
For exponential and exponential squared fogging methods, the
Density
slider allows you to
change the contrast of the colors used in fogging. Higher density makes closer portions of the
structure appear brighter and more distant ones fade more quickly into the background.
Fog options are preserved between Maestro sessions.
4.7.4
Depth Cues
When you are viewing in stereo or in perspective and you zoom in on a structure, the structure
can appear to “flatten”. This happens because the entire depth of the structure remains in the
field of view when you zoom in: it is not clipped at all, and the depth cues (eye separation or
perspective scale) are not preserved. You can preserve depth cues by selecting the
Adjust clip-
ping to preserve depth cues
option. When you do this, the front part of the structure is clipped
as you zoom in, so that you see only the parts of the structure that are “in front of you”, not the
parts that are “behind you”.
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.
The depth cues are affected by the location of the clipping planes: the closer they are to the
structure, the better the depth cues. To move the clipping planes in to fit the displayed struc-
ture, click
Enhance Depth Cues
in the
3D
tab, choose
View
→
Fog
→
Enhance Depth Cues
,
press
D
in the Workspace, or click the
Enhance
button on the
Workspace
toolbar.
You can also enhance the perception of depth with the use of ambient occlusion. This feature is
available for atom representations, and is set in the
Atoms
tab of the
Molecular Representation
panel. See
Section 7.3.1 on page 141
for details.
Chapter 5
Maestro 10.2 User Manual
79
Maestro User Manual
Chapter 5:
Building and Adjusting Structures
Maestro provides a variety of tools for building and modifying structures. The
Build
toolbar
and
Fragments
toolbar provide basic tools for building and modifying structures. In the
Build
panel, you can create molecular structures from a wide variety of predefined fragments and
modify structures and properties of atoms and residues. The
2D Sketcher
panel allows you to
draw structures in 2D. Other panels enable you to add hydrogen atoms, adjust the geometry,
connect or fuse molecules, and define centroids of groups of atoms. You can also set prefer-
ences for the behavior when certain building tasks are performed in the
Preferences
panel.
Some of the operations for building and modifying structures involve selection of atoms in the
Workspace. For information on selecting atoms, see
Chapter 6
.
5.1
The Build and Fragments Toolbars
The
Build
and
Fragments
toolbars provides quick access to tools for building, drawing, and
modifying structures. To display these toolbars, choose
Window
→
Toolbars
→
Build
or
Window
→
Toolbars
→
Fragments
, or click the relevant button on the
Manager
toolbar.
The
Build
buttons are described below, and their use is described in detail later. For a descrip-
tion of the types of toolbar buttons, see
Section 2.4 on page 17
.
Draw structures
Enter Draw mode to draw structures freehand in the Workspace. Each click in the Workspace
places an atom and connects it to the previous atom. The menu offers a choice of common ele-
ments for drawing (default C), and access to a periodic table for choosing other elements.
Delete
Delete objects in the Workspace. The button menu has several sections: one for the current
selection (
DELETE
), one for structural units to pick for deletion, one for other kinds of struc-
tural objects to delete, and one for markers and annotations.
Double-click to delete the
selected atoms.
Menu equivalent:
Edit
→
Delete
→
Pick to Delete
.
Set element
Change the element for the atoms you pick in the Workspace to the element that is selected on
the menu. The menu offers a choice of common elements (default C), and access to a periodic
table for choosing other elements.
Increment bond order
Increment the order of the bonds you pick in the Workspace by one, to a maximum of 3.