Coloring

Chimera includes many colors, and more can be created with the Color Editor or the command colordef. There is a coloring hierarchy: per-atom colors and residue-level ribbon colors override the model-level color.

• the Actions... Color menu can color atoms/bonds, ribbons, surfaces, and labels; choosing all options... opens the Color Actions dialog for more colors and finer control over which types of items are colored (background only, ribbons only, etc.)
• background color can also be set with the command background or the Background preferences
• the color command can color atoms/bonds, ribbons, surfaces, and labels
• the command ribinsidecolor specifies a separate color for the insides of protein helix ribbons
• the command modelcolor sets model-level color
• volume data display, including colors, can be controlled with Volume Viewer or the command volume

• Color Secondary Structure - set colors for helix, strand, and other segments of peptides/proteins
• Render by Attribute - show attributes such as B-factor, charge, conservation, and hydrophobicity with colors (see also the command rangecolor), radii, or worm thickness
• Rainbow (see also the command rainbow) - color progressively from one end of a chain to the other, or make each model a different color
• Color Zone - color surfaces to match nearby atoms or markers
• Surface Color (see also the command scolor) - color surfaces to show volume data values or distance from a point, axis, or plane
• Coulombic Surface Coloring (see also the command coulombic) - color molecular surfaces by Coulombic electrostatic potential

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 molecular surface attributes panel