Coloring

There are many ways to color within Chimera. Color settings can be changed for atoms, bonds, pseudobonds, models, ribbons, surfaces, labels, and the background. A hierarchy controls the visible effects of coloring operations. 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:

There are 60 built-in colors; additional colors can be created with the Color Editor or the command colordef.

Color Wells

In several situations, a small square called a color well is provided. ribbon 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 also be dragged and dropped into any color well (whether activated or not).

Several dialogs contain color wells, for example:

Several Chimera tools use color wells to specify colors. ResProp, PipesAndPlanks, and Volume Viewer are a few examples.

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: