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:
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.
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.Examples of dialogs with color wells:
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: