Maestro User Manual

Chapter 7: Changing the Appearance of Structures

Schrödinger Software Release 2015-2 

138

7.2.4

Creating and Editing Color Schemes

If you want to adjust an existing color scheme, or create a new color scheme, click 

Color

Scheme

 in the 

Atom Color

 tab of the 

Atom and Bond Coloring

 panel. The

 Color Schemes

 panel

opens, in which you can You can edit an existing color scheme, copy an existing scheme to

edit, or create a new scheme from an atom property.

To examine or edit a color scheme, first select it in the color schemes list. The list is synchro-

nized with the 

Color scheme

 option menu in the 

Atom Color

 tab of the 

Atom and Bond Coloring

panel, so the scheme you chose in that panel is the default selection in the color scheme list.

Figure 7.2. The Color Schemes panel.

New color schemes can be created from atom properties for which schemes do not already

exist. To create a new scheme that is not based on an atom property, or is based on an atom

property for which a scheme already exists, you can copy the scheme, by selecting it in the list

and clicking 

Copy

, and then edit it.

To edit a color scheme, select it in the list, and click 

Edit

. The 

Edit Color Scheme

 dialog box

opens, and allows you to change the scheme. If the scheme is not a standard color scheme, you

can change the name in the 

Name

 text box. You can modify the description of the scheme in

the 

Description

 text box.

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Chapter 7: Changing the Appearance of Structures

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Figure 7.3. The Edit Color Scheme dialog box.

Color schemes are defined in terms of rules, which are applied in order. The first rule has the

lowest priority, and can be superseded by any of the subsequent rules. Each rule is defined by

an ASL expression, and a color is assigned to that rule. The rules, their descriptions, and their

colors are listed in the 

Rules

 table.

• To add a new rule, click 

New

. A new rule is added to the end of the table.

• To insert a rule after an existing rule, select the rule and click 

Copy

. The copy is inserted

after the selected rule, and the selection is moved to the copy.

• To delete rules, select the rules and click 

Delete

.

• To revert the rules for a standard scheme to their defaults, click 

Reset All

. This button is

not available for custom color schemes.

• To change the color for a given rule, click the color cell, and choose a new color in the

Choose Color

 dialog box.

• To set the colors for multiple rules from a color ramp, select the rules, choose the color

ramp from the 

Color ramp

 option menu, and click 

Apply

.

• To change the description for a rule, edit the table cell.

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• To change the ASL expression for a rule, do one of the following:

• Edit the ASL cell directly to change the expression

• Right-click and choose 

Element

, then one of the common elements.

• Right-click and choose 

Residue Type

, then one of the standard residues.

• Right-click and choose 

Select

 to set up the ASL expression in the 

Atom Selection

dialog box.

To preview the color scheme, you can apply it by using the tools in the 

Atom Color

 tab of the

Atom and Bond Coloring

 panel.

To create a new color scheme from an atom property, click 

New

. The 

New Color Scheme

 dialog

box opens, and you can enter a name, select an atom property from the list, set the minimum

and maximum values of the property for the color scheme, the number of colors to use and

choose a color ramp. If you want some idea of the range of property values, include a molecule

in the Workspace that has a typical range, and click 

Update

. The minimum and maximum

values for this molecule are entered into the 

Min

 and 

Max

 text boxes. When you have made

settings, click 

OK

 to create the new scheme.

Figure 7.4. The New Color Scheme dialog box.

New or edited color schemes are stored in your 

Maestro user resources directory

. For informa-

tion on color scheme and color ramp files, see 

Section 13.5 on page 324

. 

You can export and import color schemes, by clicking 

Export

 or 

Import

 in the 

Color Schemes

panel. These buttons open standard file selectors, in which you can browse to the appropriate

location for the color scheme file. 

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To delete a color scheme, select it in the color scheme list, and click 

Delete

. You cannot delete

standard schemes, only custom schemes. To remove all custom schemes and revert to the stan-

dard schemes, click 

Reset All

.

7.2.5

Setting the Background Color

The default background color of the main window is black, but the color can be changed to

adjust the contrast between the background and the Workspace atoms. To change the back-

ground color, choose 

Workspace 

→

 Appearance

 in the main window and select the 

Back-

ground

 tab. You can set the color by clicking the 

color 

button and choosing a color in the

standard color selector that opens, or you can use one of the five preset colors. The preset

colors are also available from the shortcut menus in the Workspace.

7.3

Changing Molecular Representations

The molecular representation is the way in which atoms, bonds, and protein chains are drawn

in the Workspace. Atoms can be drawn as points or as spheres, and bonds can be drawn as lines

(wires) or as tubes. Protein chains can be drawn as flat “ribbons” or as tubes, representing the

secondary and tertiary structure of the protein rather than the atoms. 

The basic choice of the type of representation can be done in the 

Molecular Representation

panel and the 

Ribbons

 panel, with corresponding toolbar items for the main actions. These

choices are described in the sections below. The details of the rendering of these objects, as

well as default choices of the type of representation and other settings, are made in the 

Molec-

ular Representation

 settings group in the 

Preferences

 panel,—see 

Section 14.14 on page 378

. 

These panels are dockable panels, that open by default docked in the main window. To change

this behavior you can set preferences—see 

Section 14.1.6 on page 339

.

7.3.1

Changing the Representation of Atoms And Bonds

In the 

Molecular Representation

 panel, you can change the representation of atoms and bonds.

These representations are not entirely independent: most of the options set both the atom repre-

sentation and the bond representation. 

To open the 

Molecular Representation

 panel, choose 

Workspace 

→

 Molecular Representation

. 

At the top of the panel, you can set the representation for all atoms in the Workspace to one of

the five main representations: wire frame (lines), thin tubes, tubes, ball and stick, or CPK

(spheres). The buttons you use to set these representations are the same as on the Representa-

tion toolbar (see 

Section 7.1 on page 133

). 

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