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Atom and Bond Coloring Panel |
The Atom and Bond Coloring panel is used to change the color of atoms and bonds. Atoms and bonds can be colored by applying a single color to a group of atoms or bonds, or by applying a predefined color scheme to a group of atoms.
To open the Atom and Bond Coloring panel, you can:
Choose Workspace → Atom and Bond Coloring in the main window.
This panel is dockable, so it opens by default in the Workspace. You can change this behavior in the Preferences panel, under General – Panels.
To apply a single color to an atom or group of atoms, select Constant color under Color atoms by, choose a color from the color selector that is displayed when you click the color button, then select the atoms using the picking controls in the Apply constant color to atoms section.
The same procedure applies to the coloring of bonds, in the Bond Color tab. If you want each half-bond to have the same color as the associated atom, select Atom color under Color bonds by. The bond color is then linked to the atom color.
You can also apply a color to selected residues with the Color button on the Representation toolbar.
To apply a color scheme, rather than a single color, to atoms or groups of atoms, select Color scheme under Color atoms by in the Atom Color tab, choose a scheme from the option menu, then select atoms using the picking controls in the Apply color scheme to atoms section. You can view and edit color schemes by clicking Color Schemes, and making changes using the Color Schemes panel. For more information on the color schemes, see the Color Schemes topic.
You can also apply a color scheme to all atoms with the Color Scheme button on the Representation toolbar.
For information on using commands to color atoms, see the Coloring Atoms Using Maestro Commands topic.
The default color scheme can be set in the Preferences panel, under Molecular representation – Atoms and bonds.
In this tab you can set atom colors.
Choose the means by which atoms are colored. The options are:
Color scheme—Color atoms using a defined color scheme, which you can select from the option menu. For some color schemes (which usually include the word Custom), a color option menu is displayed below the schemes option menu, so that you can choose the custom color. The option menu has a list of available colors.
If you want to modify or add a color scheme, or view the color scheme definitions click the Color Schemes button, which opens the Color Schemes dialog box.
Constant color—Color atoms with the same color, which you can choose by clicking the color button and making a choice in the color selector that opens. The color button is not shown until you select this option.
In this section you can use the standard picking tools to color the atoms by the chosen color scheme or with the chosen constant color. The section name changes when you chose an option under Color atoms by, to reflect the choice you made.
These options allow you to choose the method for coloring bonds:
In this section you can use the standard picking tools to color the bonds by the chosen method. The section name changes when you chose an option under Color bonds by, to reflect the choice you made.
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