The color command selectively colors bonds (atoms), labels, molecular surfaces, and van der Waals surfaces. Nonmolecular graphical objects are unaffected by the color command. Using ~color sets the color to none (no color assigned).
Color_name is a built-in name or a name defined previously with colordef. A special color name is colorpanel, which refers to the color currently defined in the Color Editor. Another special color_name is byatom, which sets color based on element (inferred from the atom names):
| atom name prefix | color |
|---|---|
| C | gray |
| N | blue |
| O | red |
| S | yellow |
| H,D,0-9 | white |
| F,CL,BR,I | magenta |
| B,FE | gray |
| others | cyan |
The optional specifiers b, l, s, and v designate bonds (atoms), labels (atom labels), molecular surfaces, and van der Waals surfaces, respectively. When b is used to indicate "bonds," in actuality the specified atoms are colored and the bonds merely reflect the color(s) of the atoms. The specifier l allows atom labels to be colored differently than the associated atoms. (Note that the colors of bond labels and pseudobond labels are not affected. One way to color such a label is to select the bond or pseudobond and use the Selection Inspector to change its label color.) In the absence of a specifier, the atoms, labels, and surfaces are all affected. The specifiers do not need to be comma-separated when used with ~color.
The atom-spec indicates which atoms (and/or associated labels or surfaces) are to be colored. If no atom-spec is given, all atoms (and/or all their labels or surfaces) are affected.
In Chimera, visible color is determined by a hierarchy: per-atom colors overrule color settings at the model level. Even when entire models are specified, the color command always sets colors at the atom level. The command modelcolor sets colors at the model (or submodel) 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.
Examples:
color green #2:his- color all histidine residues in model 2 green, as well as any associated labels, molecular surface, and van der Waals surface
color magenta,s #3- color the surface of model 3 magenta
~color bl #0:4- remove the color assignments of atoms and their labels in the fourth residue of model 0 (the visible color will default to the per-residue color, or if there is no per-residue color assignment, to the model-level color)
color red @/color=blue- color red every atom that is blue (and any labels and surfaces associated with those atoms)
See also: colordef, colorrename, label, surface, vdw, rainbow, ribcolor, modelcolor, surfcolor, tcolor, the Actions menu