Maestro User Manual

Chapter 7: Changing the Appearance of Structures

Schrödinger Software Release 2015-2 

142

Figure 7.5. The Molecular Representation panel.

Under 

Atom representation

, you can choose between three options for the representation of

atoms, with the corresponding bond representation. The options are:

•

None

—no representation of atoms, with bonds represented as wires.

•

Ball & Stick

—represent atoms as spheres, and bonds as tubes.

•

CPK

—represent atoms as large spheres, using the van der Waals radii of the atoms for the

sphere radii. The bond representation is not changed if you set it with the 

Bond represen-

tation

 options; otherwise it reverts to wire.

To apply the atom representation, use the picking tools in the 

Apply current representation to

atoms

 section to select atoms to apply the representation. 

Under 

Bond representation

, you can choose between four options for the representation of

bonds, with the corresponding atom representation. The options are:

•

None

—no representation of bonds. This option only sets the bond representation; the cur-

rent atom representation remains in effect.

•

Wire

—represent bonds as wires (lines), with no representation of atoms.

•

Thin tube

—represent bonds as thin tubes, with atoms represented by spheres the same

size as the tubes (i.e. caps to the tubes).

•

Tube

—represent bonds as tubes, with atoms represented by spheres the same size as the

tubes (i.e. caps to the tubes).

You can mix representations within a single molecule by picking. When you do so, the half of

each bond that is attached to each atom that is picked is represented with the chosen bond style.

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You can apply a molecular representation to atoms using the buttons on the 

Representation

toolbar.

Click the arrow next to any of the buttons to pick the structural unit to apply the representation

to. Double-click the button to apply the representation to the selected atoms, or to all atoms if

there is no selection. 

For atoms represented in CPK, the depth view can be enhanced using an approximate calcula-

tion of ambient occlusion, which takes into account the ambient lighting that is blocked by

nearby atoms. To enable the enhancement, select 

Enhanced depth view

 under 

Workspace –

Depth view

 in the 

Preferences

 panel or from the 

Workspace

 menu in the main window, or press

D

 when the pointer is in the Workspace. 

7.3.2

Rendering Proteins, DNA, and RNA as Ribbons

In the 

Ribbons

 panel you can display protein backbones as a ribbon diagram and DNA and

RNA as a ladder diagram. Displaying ribbons can simplify the analysis of secondary and

tertiary structures. You can choose from seven ribbon styles and nine color schemes, and apply

the ribbon style by picking or using the 

Atom Selection

 dialog box. You can mix representa-

tions within a single protein by picking. 

To open the 

Ribbons

 panel, choose 

Workspace 

→

 Ribbons

.

Figure 7.6. The Ribbons panel, showing tools for color schemes.

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Chapter 7: Changing the Appearance of Structures

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Ribbons are defined by a style and a color scheme. The choices of style are:

•

Cartoon

—display loops as thin tubes, sheets as arrows and helices as ribbons.

•

Ribbon

—thin, curved flat surface that follows the backbone.

•

Tube

—curved tube that follows the backbone.

•

Thin Tube

—thin curved tube that follows the backbone. 

•

Curved Line

—curved line that follows the backbone. 

•

CA Trace

—straight line that connects alpha carbon atoms. 

•

CA Trace Tube

—straight tube that connects alpha carbon atoms. 

The 

Color scheme

 option menu provides a range of properties which can be used to select the

color scheme, such as residue properties and secondary structure. Each of these has a

predefined set of colors that is applied to the ribbon.

With the exception of the 

CA Atom Color

 scheme, the color schemes are described in the 

Color

Scheme

 tab of the 

Atom Coloring

 panel (see 

Section 7.2.3 on page 135

). In the 

CA Atom Color

scheme, the ribbon is colored with the current color of the alpha carbon atoms. Thus, if you

change the color of certain residues and reapply this color scheme, the section of the ribbon for

which you changed the residue color changes color to match. 

In the 

Ribbon

 or the 

Cartoon

 style, helices can be colored the same color on both sides of the

ribbon, or the inside can be colored gray. The choice between these two is made by setting a

preference in the 

Molecular Representation – Ribbons

 section of the 

Preferences

 panel (see

Section 14.14.2 on page 380

).

Two of the color schemes have other choices that you can make. The controls for these choices

are displayed in the panel when you choose the color scheme—see 

Figure 7.6

—and are

described below. 

•

Constant color

—Choose the color to use for coloring the ribbons. This option menu is

only available if you choose 

Constant color

 from the 

Color scheme

 option menu. 

•

Residue position limits

—These options allow you to set residue number limits for apply-

ing the 

Residue position

 color scheme, and are only available when that scheme is chosen

from the 

Color scheme

 option menu. Residues with residue numbers outside the range

are colored with the color for the end of the range. Insertion codes are ignored.

•

Lower limit

—Select this option to set the lower limit for coloring, and enter the low-

est residue number in the text box.

•

Upper limit

—Select this option to set the upper limit for coloring, and enter the high-

est residue number in the text box.

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