Coloring

There are many ways to color within Chimera. Color settings can be changed for atoms, bonds, residues, models, labels, surfaces, pseudobonds, and objects. A hierarchy controls the visible effects of any coloring operation. Briefly, atom colors assigned on a per-atom basis and ribbon colors assigned on a per-residue basis override the model-level color.

Some simple approaches:

• the Color section of the Actions menu can be used to color atoms/bonds, ribbons, surfaces, and labels
• the commands color and rainbow can be used to color atoms/bonds, labels, and surfaces
• the commands ribcolor and rainbow can be used to color ribbons
• the command modelcolor can be used to color molecule models

Color Wells

In several situations, a small square called a color well is provided. Clicking on a color well opens the Color Editor and activates the well so that it reflects any color changes within the Color Editor. The border of the color well turns white to signify activation. The color defined in the Color Editor can also be dragged and dropped into any color well (whether activated or not). Several dialogs contain color wells, for example:

• the Selection Inspector lists what items are selected, shows their properties (including color), and allows their properties to be changed
• the molecule model attributes panel includes model-level color
• the pseudobond attributes panel includes pseudobond group-level color

Surface Color Source

Atoms and models have surface color assignments that can differ from each other and from their own color assignments. The default behavior is for the visible surface color(s) to match the visible atom color(s), determined by the coloring hierarchy mentioned above. The level in the hierarchy used as the source for visible surface colors can be changed with:

• the command surfcolor
• the surface attributes panel