Usage:
( color | colour )  color_name[,a][,f][,r][,s][,v][,l][,la][,lr][,lb][,b]  atom-spec

Usage:
( ~color | ~colour )[,a][,f][,r][,s][,v][,l][,la][,lr][,lb][,b]  atom-spec

The color command sets colors of atoms, bonds, ring fill, ribbons, labels (3D), molecular surfaces, VDW surfaces, and nonmolecular surface models. The command ~color sets the color to none (no color assigned); assignments at other levels in the coloring hierarchy may become visible. See also: colordef, ribinsidecolor, scolor, sop colorCopy, modelcolor, rainbow, rangecolor, transparency, background, set, setattr, msc, coloring

The color_name can be:

• any of 169 built-in color names
• a name defined previously with colordef
• a Tk color code such as #7fffd4 or #b0b030306060 (more examples)
• an R,G,B or R,G,B,A tuple, where R is the red component, G is the green component, B is the blue component, and A is the opacity (1 – transparency), each in the range 0-1. The values should be separated by commas only, not spaces. Example: 1,0.25,0.8,0.3
• colorpanel, fromeditor, or editor - the color currently defined in the Color Editor

• none - no color assigned (like using ~color); assignments at other levels in the coloring hierarchy may become visible
• byatom or byelement - a color-by-element scheme; does not apply to ribbons or residue labels. The color names are the same as the element symbols. For example, a colored-by-element sulfur atom may look yellow, but is actually the color S (slightly different than yellow).
• byhet or byhetero - same as byatom, except leaving carbon atoms unchanged

• a - atoms (and normally, bond halves are colored to match the flanking atoms; see b for bonds-only coloring)
• f - ring fill
• r - ribbons
• s - molecular surfaces and nonmolecular surface models
• v - VDW surfaces
• l - atom and residue labels
• la (or al) - atom labels
• lr (or rl) - residue labels
• lb (or bl) - bond labels
• b - bonds only (not the flanking atoms), turning off halfbond mode; ~color with the ,b specifier turns halfbond mode back on; equivalent to using bondcolor

The atom-spec indicates which atoms (and/or associated bonds, ribbon segments, surface patches, etc.) should be affected, and a similar specification can be used for nonmolecular surface models. If no specification is given, all applicable items are affected.

In Chimera, visible color is determined by a hierarchy. Color sets atom, atom label, and surface colors at the atom level, and ribbon and residue label colors at the residue level. Modelcolor sets colors at the model level. Surfcolor sets which level is used as the source for visible surface colors; this must be the atom level for color to control the visible surface color.

Transparency can be set independent of color with the transparency command.

Examples:

color green #2:his

color #ff00ff,r,s #3

~color,a,l #0:4

color cyan,r helix; color magenta,r strand; color gray,r coil