Maestro User Manual

Chapter 7: Changing the Appearance of Structures

Schrödinger Software Release 2015-2 

148

The 

Environment map

 option menu provides a selection of environments (“pictures”) that are

shown as reflections on the surfaces of the objects in the Workspace. This menu is only present

when the OpenGL level is 2.1.

You can restore the default material values for an object by clicking 

Restore Defaults

.

Some combinations of lighting and material are available from the 

Style

 toolbar—see

Section 7.6 on page 154

.

Special effects can be added to structures in the 

Effects

 tab. There are four effects available,

which can be combined. These effects apply to the entire screen (Workspace). Other effects

can be added to specific objects, as highlights—see 

Section 8.5 on page 168

. Some of the

screen effects are also available as preferences, though with limitations. 

Figure 7.9. The Effects tab in the Appearance panel.

•

Antialiasing

—smooth the edges of objects so they don't appear jagged. This effect does

not antialias semi-transparent objects. The 

Full-scene antialiasing

 preference

(

Section 14.4.16 on page 355

) does, but it does not antialias spheres and cylinders (balls

and sticks). For the smoothest edges, use both the preference and the screen effect.

•

Ambient occlusion

—enhance the perception of depth by taking into account the ambient

lighting blocked by nearby objects, pixel by pixel. The 

Enhanced depth view

 preference

(

Section 14.4.12 on page 354

) uses ambient occlusion based on atoms, and is only avail-

able for structures in CPK representation. This option is most useful for large structures

in CPK representation and with molecular surfaces.

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Chapter 7: Changing the Appearance of Structures

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Figure 7.10. Use of ambient occlusion. From left to right: no effect, Enhanced depth view 

preference (atom based), Ambient occlusion screen effect (pixel-based).

You can set the intensity of the darkening effect with the 

Intensity

 slider and box. The

intensity is represented as a percentage, with 0 corresponding to no effect. You can also

change the range of the effect, with the 

Radius

 slider and box. Any screen object within

the specified radius of a pixel is considered to occlude the pixel. Thus, the smaller the

radius, the more local and “sharp” the effect. At a very small radius, the effect is like

outlines.

•

Outlines

—Add a thin outline to objects in the Workspace. You can set the width of the

outline (in pixels) in the 

Width

 text box, and you can set the color with the color button.

•

Cartoon shading

—Use cartoon shading, in which the color or shading is done in steps

rather than continuously. You can set the number of steps in the 

Steps

 text box.

This tab is not present if the OpenGL level is 1.2, as it requires features that are not present at

this OpenGL level.

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7.5

Displaying and Undisplaying Atoms

Maestro provides a range of tools for selectively displaying or undisplaying atoms. These tools

are available in the 

Display/Undisplay Atoms

 panel, on the 

Display

 toolbar, and on the Selection

shortcut menu. Maestro also provides tools for displaying atoms that are related by crystallo-

graphic symmetry and alternate positions for atoms.

7.5.1

The Display Atoms Toolbar

Many of the operations for displaying or undisplaying atoms are available from the 

Display

Atoms

 toolbar, and some of them are only available from the toolbar. The toolbar buttons are

described in brief below, and their use is described in the following sections. 

7.5.2

Selectively Displaying Atoms

You can display or undisplay (hide) atoms using the toolbar buttons or the 

Display/Undisplay

Atoms

 panel. These tools allow you to select the atoms that are displayed or are not displayed

in the Workspace. For example, you can hide from view all atoms, user-defined atom subsets,

or predefined subsets such as protein backbones, side chains, water molecules, or hydrogen

atoms. 

Display Sel 

Display only the selected atoms. This button has a menu from which you can choose a struc-

tural unit to use when picking atoms for display. Choose a structural unit, then click on an 

atom to display the atoms in that unit only. Double-click to display only the selected atoms, or 

all atoms if there is no selection. 

Display Only 

Display only the atoms in a particular category. From the button menu, you can select a cate-

gory of atoms to display, or open the 

Atom Selection

 dialog box to select atoms to display.

Also Display 

Add the atoms in a particular category to the display. From the button menu you can select a 

category of atoms to add to the display, or open the 

Atom Selection

 dialog box to select atoms 

to add to the display.

Undisplay 

Undisplay (hide) atoms in a particular category. From the button menu you can select a cate-

gory of atoms to undisplay, or open the 

Atom Selection

 dialog box to select atoms to undis-

play. 

Within 

Display residues within a specified distance of the currently displayed atoms. Entire residues 

that have any atoms within this distance of the displayed atoms are added to the display. From 

the button menu you can select a specific distance, or open a dialog box to enter a distance. 

Clicking the button performs the action.

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