Molecular Representation Preferences

These options control the default representation of atoms and bonds.

Default representation option menu

This option menu allows you to set the default representation used for newly built structures to one of the five representations: Wire, Thin tube, Tube, Ball & Stick, or CPK. Atoms added to a structure inherit the representation of the structure. If you import a file in Maestro format and it includes graphical information, the representation saved in the file is used rather than the defaults.

Default color scheme option menu

This option menu allows you to set a default color scheme for atoms and bonds. For some color schemes (which usually include the word Custom), a color button is displayed next to the schemes option menu, so that you can choose the custom color in a standard color chooser. The color schemes can be changed using the Color Schemes settings.

Wire settings section

The Wire representation has a range of options for the style, representation of bonds, and display of bond orders.

Show bond orders option

Draw multiple lines when there are multiple bonds between atoms. When this option is off, only a single line is drawn, regardless of the bond order.

Scale wire width option and text boxes

If you want the wire width to scale as you zoom in, select Scale wire width. You can adjust the minimum and maximum wire (line) width in the Min and Max text boxes. The values are given in pixels, and there are limits on how much you can change these values that are determined by the OpenGL implementation on your computer.

Wire width slider

Set the width of wire in pixels.

Style options

The Style settings control how color is applied to bonds.

• Split—The bonds are split, and each half is colored with the color of the nearest atom.
• Blend—The color is progressively changed along the bond from the color of one atom to the color of the other.

Smoothing options

These options request smoothing of the graphical display of the bonds. When Show bond orders is on, those bonds that are drawn with widths greater than one are not smoothed.

Tube/Stick/CPK settings section

This section has a set of sliders for setting the diameters of the tubes and spheres used in these three representations. The van der Waals radii used for the spheres are taken from the RDKit package (https://rdkit.org/).

Show bond orders option

Draw multiple tubes when there are multiple bonds between atoms. When this option is off, only a single tube is drawn, regardless of the bond order.

Tube representations:

The Tube radius and Thin tube radius sliders set the radius of the tubes in angstroms.

Ball & Stick representation:

The Ball percentage slider sets the percentage of the van der Waals radius of the atoms that is used to determine the size of the spheres.

The Stick radius sets the radius of the sticks in angstroms.

CPK representation:

The CPK percentage slider sets the percentage of the van der Waals radius of each atom that is used to determine the size of the spheres.

Restore Defaults button

Restore the default values for the atom and bond representation.

These settings control the defaults for display of ribbons.

Default style option menu

This option menu provides a choice of seven display styles: Cartoon, Ribbon, Tube, Thin Tube, Curved Line, CA Trace, and CA Trace Tube

Default color scheme option menu

This option menu provides a range of properties that 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. The color schemes are explained in Coloring Atoms. If you choose Single Color, a color button is displayed, which you can click on to change the color.

Quality options

Set the quality of the ribbon rendering. The choice controls the smoothness of the ribbons.

Strands are drawn options

Select Smoothed to apply smoothing to the drawing of the strands, which as a result might not pass through the alpha carbons. Select Passing through alpha carbons to force the strands to pass through the alpha carbons, at the loss of some smoothness in the appearance.

Use simplified representation when moving option

Use a lower-quality ribbon representation when translating or rotating. You might want to set this preference if translation or rotation of structures is slow when ribbons are displayed, to improve the speed.

Blend ribbon colors option

Select this option to create a smooth color transition on the ribbons between residues.

Helix interior options

Select an option for coloring the interior of helices (and ladders). The two options are to use gray for the inside, or the same color as the outside, which is determined by the color scheme.

Ribbon width slider and text box

Set the width of ribbons in angstroms.

Ribbon thickness slider and text box

Set the thickness of ribbons in angstroms.

Strand width slider and text box

Set the width of strands in angstroms.

Strand thickness slider and text box

Set the thickness of strands in angstroms.

Thin tube width slider and text box

Set the width of thin tubes in angstroms. These tubes are used in Cartoon and Thin Tube representation.

Thick tube width slider and text box

Set the width of thick tubes in angstroms. These tubes are used in Tube representation.

Ladder width slider and text box

Set the width of the rungs of the ladder for DNA and RNA. The sides of the ladder are controlled by the ribbon settings.

Restore Defaults button

Restore the default values for ribbon representation.

These options allow you to manage the color schemes used for coloring structures. You can view the descriptions of color schemes; create, copy, delete, and edit color schemes; and import and export color schemes. Color schemes are stored in your Maestro user resources directory.

List of schemes

All schemes, standard and custom, are listed in the list of schemes.

You can select a single row in the list of schemes, and the name and description are displayed below. You can drag this row to a new location in the list, and you can apply an action to the row with one of the buttons Edit, Copy, or Delete.

For a list of standard schemes and their descriptions, see the Coloring Atoms topic.

Editing buttons

The buttons to the right of the list can be used to edit, store, or load color schemes, which are stored in text files.

When you make any changes to the color scheme, or add color schemes, the changes are stored in your Maestro user resources directory (see Customizing Color Scheme Files).

Edit button

Edit the selected color scheme (standard or custom). Opens the Edit Color Scheme Dialog Box.

New button

Add a new color scheme based on an atom property. A message is displayed if there are no atom properties for which a color scheme is not defined. Opens the New Color Scheme Dialog Box.

Copy button

Make a copy of an existing color scheme, which can then be edited as a custom scheme. The copy is added to the end of the list, and the name has an index number appended. You can edit the name when you edit the scheme.

Delete button

Delete the selected scheme, after confirmation. This button is only available when you select a custom scheme.

Import button

Import a color scheme from a file (.sch). The imported scheme is added to the end of the list, and the name is made unique if necessary. Opens a file selector, so you can navigate to and select the file.

Export button

Export a color scheme to a file (.sch). Opens a file selector, so you can navigate to a location and name the file.

Reset All button

Remove all custom color schemes and revert the standard schemes to those in the installation (Maestro resources directory). This action must be confirmed in the dialog that is displayed, as it cannot be undone.

Color scheme text box

Displays the name of the selected color scheme. The name can be changed in the Edit Color Scheme Dialog Box (click Edit to open).

Description text area

Displays the description of the selected color scheme. Noneditable, but can be selected for copy/paste. The description can be edited in the Edit Color Scheme Dialog Box (click Edit to open).