Chimera Commands Index

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

( ~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:

The color command also accepts: The assignment can be restricted with one or more specifiers: In the absence of a specifier, all of the above are affected except bonds-only, and halfbond mode is turned on so that bond halves are colored to match the flanking atoms. However, VRML models, 2D Labels, and pseudobonds and their labels are not affected. A pseudobond or its label can be colored by selecting the pseudobond and using the Selection Inspector to change its color or label color.

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.


color green #2:his
- color all histidine residues in model 2 green, as well as any associated labels, ribbon segments, surface patches, etc.
color #ff00ff,r,s #3
- color ribbons and surface of model 3 #ff00ff (magenta)
~color,a,l #0:4
- remove the color assignments of atoms and their labels in residue 4 of model 0 (the color will default to the model-level color)
color cyan,r helix; color magenta,r strand; color gray,r coil
- color protein ribbons by secondary structure