Maestro User Manual

Chapter 4: Viewing the Workspace

Schrödinger Software Release 2015-2 

78

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. 

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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. 

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