Maestro User Manual

Schrödinger Software Release 2015-2

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Chapter 7

Maestro 10.2 User Manual

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Maestro User Manual

Chapter 7:

Changing the Appearance of Structures 

Maestro provides a wide selection of options for displaying structures. For example, you can

change the color of some or all of the atoms, change the molecular representation in which the

atoms are depicted, label atoms by their properties, or selectively undisplay certain atoms so

that you can better examine small subsections of a structure. 

7.1

The Representation Toolbar

Many of the features for changing the appearance of structures are available from the 

Repre-

sentation

 toolbar. The toolbar buttons are described in brief below, and their use is discussed in

the following sections.

Ribbon 

Show, hide, or color ribbons. From the button menu you can choose to display ribbons for all, 

selected, or displayed residues; delete ribbons; and display various combinations of atoms that 

are associated with the ribbons; and choose various coloring schemes for the ribbons. Click to 

pick residues for display of ribbons. Double-click to display ribbons for the selected atoms, or 

for all atoms if no atoms are selected.

Wire 

Draw bonds in wire frame representation. From the button menu you can select a structural 

unit to use when picking atoms to display in wire representation. Double-click to apply to the 

selected bonds, or to all bonds if there is no selection. 

CPK 

Draw atoms in CPK representation. From the button menu you can select a structural unit to 

use when picking atoms to display in CPK representation. Double-click to apply to the 

selected atoms, or to all atoms if there is no selection.

Ball & Stick 

Draw atoms and bonds in ball-and-stick representation. From the button menu you can select a 

structural unit to use when picking atoms to display in Ball & Stick representation. Double-

click to apply to the selected atoms, or to all atoms if there is no selection. 

Tube 

Draw bonds in tube representation. From the button menu you can select a structural unit to 

use when picking atoms to display in tube representation. Double-click to apply to the selected 

bonds, or to all bonds if there is no selection. 

Thin Tube 

Draw bonds in thin tube representation. From the button menu you can select a structural unit 

to use when picking atoms to display in tube representation. Double-click to apply to the 

selected bonds, or to all bonds if there is no selection.

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Chapter 7: Changing the Appearance of Structures

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7.2

Changing Atom, Bond, and Background Color

Changing the color of a structure can help you to visualize its properties and its three dimen-

sional structure. The 

Atom and Bond Coloring

 panel allows you to apply a new color to all or

some of the Workspace atoms and bonds, or to use predefined or user-defined schemes to color

specific atom groups. You can also use the shortcuts available in the toolbar to change the atom

coloring. The default color is set in the 

Preferences

 panel—see 

Section 14.14.1 on page 378

.

To open the 

Atom and Bond Coloring

 panel, choose 

Workspace 

→

 Atom and Bond Coloring

. 

This panel is a dockable panel, that opens by default docked in the main window. To change

this behavior you can set preferences—see 

Section 14.1.6 on page 339

.

Figure 7.1. The Atom and Bond Coloring panel, showing both tabs.

7.2.1

Applying a Single Color to Atoms and Bonds

To apply a single color to some or all atoms or bonds in the Workspace, you can use the tools in

the 

Atom Color

 or 

Bond Color

 tab. Select 

Constant color

 under 

Color atoms by

 or 

Color bonds

by

, then select a color by clicking 

the color button 

in the 

Atom Color

 tab to open a standard

color selector, or clicking the color button in the 

Bond Color

 tab to display a color palette. Once

you have selected a color, use the picking tools or the selection button in the 

Apply constant

color

 section to apply the color to selected atoms or bonds. For a wider range of bond colors,

Color Scheme 

Color all atoms with a chosen color scheme. From the button menu you can choose the 

scheme, as defined in the 

Color Schemes

 tab of the 

Atom Coloring

 panel. The custom color 

schemes for carbon atoms and ligands are on a submenu. 

Color 

Color the picked residues with a constant color, which you can choose from the button menu. 

Double-click to apply the color to the selected atoms, or to all atoms if there is no selection.

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Chapter 7: Changing the Appearance of Structures

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the color palette has an 

Advanced

 button, which opens the 

Choose Color

 dialog box, where you

can modify the palette and choose colors by RGB value.

You can also apply a color from the 

Color 

button menu on the 

Representation

 toolbar.

This button displays a menu from which you can choose from a selection of colors. The color

choice is persistent. You can then pick residues to apply the color, or double-click the button to

apply the color to all atoms. If the color you want to use is not on the menu, you can use the

Atom Color

 tab to select the color. The RGB value of the colors in the color palette is displayed

in a tool tip. For information on customizing the colors, see 

Section 13.5.2 on page 325

.

7.2.2

Coloring Bonds by Atom Colors

If you want half-bonds to be colored by the atom color, select 

Atom color

 under 

Color bonds by

in the 

Bond Color

 tab. This option ties the bond color to the atom color, regardless of how the

atom is colored.

7.2.3

Using Color Schemes to Color Atoms

To apply coloring to some or all Workspace atoms using one of Maestro’s predefined color

schemes, or a custom color scheme, select 

Color Scheme

 under 

Color atoms by

 in the 

Atom

Color

 tab, then select the scheme from the option menu below this option. If you choose one of

the schemes with custom colors (for carbons or ligands), choose the color from the custom

color option menu (labeled 

Carbon color

 or 

Ligand color

). Once you have selected a scheme,

use the picking tools to select the atoms you wish to color.

You can apply a color scheme to all atoms in the Workspace from the 

Color all atoms by

scheme

 button menu in the toolbar. 

When you click on the arrow to the right of the button, a menu is displayed from which you can

choose the scheme. The custom carbon and custom ligand schemes are in submenus. The color

scheme is applied when you make your menu choice. 

If you want to see a description of the color scheme, click 

Color Schemes

, which opens the

Color Schemes

 panel. This panel allows you to view the description of the color scheme. For

details of the actual colors applied, click 

Edit

 in this panel. The 

Edit Color Schemes

 dialog box

lists the details of the colors and the criteria used to apply them. Use of this panel is described

below. The standard color schemes are described in 

Table 7.1

. 

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