Chimera Commands Index

( rangecolor | rangecolour ) attr_name[,a][,r][,s][,v][,l][,la][,lr] [key] value1 color1 value2 color2 [... valueN colorN] atom-spec

Rangecolor shows the values of an attribute such as B-factor or hydrophobicity with color gradations. The attribute is specified by name (attr_name) and must be numerical (see examples). The related tool Render by Attribute provides a graphical interface for coloring by attribute values. See also: color, colorkey, rainbow, coulombic, scolor, transparency, defattr, setattr, msc, Render by Attribute, examples on the Chimera website: Mapping Sequence Conservation, Coloring by NMR Chemical Shift Perturbation

At least two value/color pairs must be supplied. Pairs do not need to be ordered by value. Values (value1, value2, etc.) can be specified directly or with the special words:

value indicator meaning
min minimum value among the specified atoms
max maximum value among the specified atoms
mid average of min and max
novalue no value assigned for the attribute

A pair specified with novalue does not contribute toward the minimum of two pairs because the corresponding color is not involved in any ranges; it is only used to color items with no value for the specified attribute (for example, nucleic acid residues do not have kdHydrophobicity values). When an atom attribute is used to color ribbons, the ribbon segment for each residue is colored according to the average of the values for atoms in the residue. In all cases, the reported min, mid, and max values describe the original attribute rather than any derived quantity such as an average.

Each color name (color1, color2, etc.) can be any color name that specifies a single color.

The atom-spec indicates which atoms (and/or associated labels, surfaces, or ribbon) are to be colored. If no atom-spec is given, all atoms (and/or their associated labels, surfaces, or ribbon) are affected.

While atom-spec indicates the scope of coloring, one or more specifiers can be used to indicate which types of items should be colored:

In the absence of a specifier, all of the above are affected. Other kinds of surfaces, 2D Labels, and bond labels are not affected.

The key option brings up the Color Key tool, filled in with the appropriate colors and values, and set to Use mouse for key placement for creating/positioning the color key in the graphics window. The mouse setting can be toggled to allow moving models with the mouse.

In Chimera, visible color is determined by a hierarchy. Rangecolor sets atom, atom label, and surface colors at the atom level, and ribbon and residue label colors at the residue level.


rangecol bfactor,s key min blue 20 white 40 red
- color the molecular surface (only) by the atom attribute named bfactor, from blue for the minimum value, to white for 20, to red for 40 and above; call Color Key, filled in with those values and colors
range kdHydrophobicity min lime green max orange novalue magenta
- color from lime green to orange by increasing values of the residue attribute named kdHydrophobicity; color any residues without hydrophobicity assignments magenta