Coloring

There are many ways to color within Chimera. Colors can be changed for atoms, bonds, pseudobonds, ribbons, surfaces, labels, models, and the background. A hierarchy controls the visible effects of coloring operations. Briefly, atom-level colors and residue-level ribbon colors override the model-level color.

Some simple approaches:

• atoms/bonds, ribbons, surfaces, labels, and the background can be colored using the menu (Actions... Color)
• atoms/bonds, ribbons, surfaces, and labels can be colored with the command color
• ribbons can be colored with the command ribcolor
• model-level color can be changed with the command modelcolor
• background color can be changed with the command set bg_color
• background color can be set in the Background preferences

Many additional tools or commands assign colors according to the properties of molecular structures or other data. Color Secondary Structure, Rainbow, Render by Attribute, and Surface Color are just a few.

Many dialogs contain color wells. 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. Clicking another color well activates the newly clicked well and deactivates any previously activated wells, whereas Shift-clicking a color well toggles the activation status of that well without changing the activation status of any other color wells.

The color defined in the Color Editor can be dragged and dropped into any color well (whether activated or not). A color can also be dragged from one color well and dropped in another in the same or a different Chimera dialog.

• the Selection Inspector
• the Model Panel
• FindHBond

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