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Command: color, rainbow

The color command colors atomic models, including atoms, bonds, pseudobonds, cartoons, and molecular surfaces. It can also apply to nonmolecular surfaces, depending on the type of coloring:

See examples below. See also: transparency, mlp, surface, volume, Molecule Display Toolbar, initial colors, color names, palettes

Subcommands of color:

Simple Coloring

Usage: color  spec   colorname   general-options

Simple coloring applies to atomic models, including cartoon and molecular surface representations, and volume data (map) displays. The colorname can be:

Sequential Coloring (Rainbow)

Usage: color  atom-spec   sequential  level  [ palette  palette ]  general-options
– or –
Usage: rainbow  atom-spec  [ level ] [ palette  palette ]  general-options

The sequential coloring method (synonym rainbow, see examples) applies a series of colors at the specified level:

For rainbow only, the level can be omitted and defaults to residues. Sequential coloring applies to all atoms within the affected residues, chains, or models even if fewer atoms are specified, but can be restricted to certain representations with the target option.

Coloring by Map Value

Usage: color  spec  map  map-model  [ offset  d ]  palette-options   general-options

Coloring by map value applies to surfaces only, both molecular and nonmolecular (such as volume isosurfaces). The color-value mapping is specified with palette options. The offset d is how far out from each surface vertex, along its normal, to evaluate the data (default 0.0 Å). An offset of 1.4 Å is typically used for coloring a molecular surface by electrostatic potential. The rationale for looking outward is that the values at the centers of any interacting atoms are more relevant than those at their surfaces. By default, a molecular surface shows where the surface of a spherical probe of radius 1.4 Å can lie, the solvent-excluded surface. An offset of 1.4 Å approximates the solvent-accessible surface, about as close as the probe center can get to the molecule.

Coloring by Zone

Usage: color  surf-model  zone  atom-spec  [ distance  cutoff ]

Coloring by zone to match nearby atoms or markers applies to nonmolecular surfaces only. The cutoff is specified in physical units of distance, typically Å (default 2.0). When multiple specified atoms fall within the cutoff distance of a surface vertex, the vertex will be colored to match the closest one. Vertices not within the cutoff of any of the atoms are assigned the default color of the surface model (single-color mode).

General Options

target  string
Specify coloring only a subset of the possible displays of a given atom, residue, etc. The string can be any combination of the following letters, without commas or spaces: The default is all of the above (target abcsp), except that surface coloring is not yet implemented for sequential coloring (if atoms have been colored sequentially, however, the surface can be colored to match the atoms with the command: color fromatoms target s).

Alternatively, for simple coloring only, a single target can be specified with a keyword immediately following the colorname:

halfbond  true | false
By default, bonds are shown in halfbond mode, with color and transparency settings from the flanking atoms. Turning halfbond mode off for a bond (or pseudobond) reveals its own color/transparency settings independent of the atoms. This option can be used to toggle halfbond mode regardless of whether the command colors any bonds. It affects only the specified bonds (not pseudobonds), except obeying the target setting when it includes p.
transparency  percent
Set transparency to the specified percent, where 0% is completely opaque and 100% is completely transparent. Existing transparency is not changed unless this option is used or the colorname explicitly specifies alpha (opacity). An alpha value overrides this option if both are given. Note that the transparency command can be used to set transparency apart from color.

Palette Options

A palette is an ordered set of colors or value,color pairs used for sequential coloring or coloring by map value.

palette  palette
Specify a palette as one of the following:
range  low,high | full
For numerical data only (not sequential coloring), what values should map to the extremes of the palette (default full, the minimum and maximum values for the items to be colored). Alternatively, low and high values separated by a comma only can be supplied. When multiple models are colored in a single command, the full range is determined separately for each model.


color /d & helix  sky blue  target c
– or –
color /d & helix  sky blue  cartoons
- color chain D helices sky blue, cartoons only (not atoms, etc.)
color /A,B:12,260-275  hot pink  target a
– or –
color /A,B:12,260-275  hot pink  atoms
- color residues 12 and 260-275 in chains A and B, atoms/bonds only
color pbonds  yellow
- color all pseudobonds yellow
color C  bymodel  targ a
- restore original model coloring to all carbon atoms
color seq res
– or –
rainbow res
– or –
- rainbow-color residues blue → red along each biopolymer chain
color #3 seq chain  palette cyan
– or –
rainbow #3 chain  palette cyan
- color the chains in model 3 from a medium cyan through white to dark maroon
color seq polymers  targ c  palette cornflowerblue:red:gold
– or –
rainbow polymers  targ c  palette cornflowerblue:red:gold
- color the unique biopolymers in each atomic model, cartoons only, along the range cornflower blue → red → gold (chains that are the same biopolymer will be the same color)
open 1qmv; rainbow protein chain palette paired-10
- color the protein 10-mer in PDB entry 1qmv using the 10-color version of the “paired” ColorBrewer palette

Defining and Listing Colors

color name  cname  color-spec

color deletecname | custom )

color listall | builtin | custom ]

color show  cname

The command color name assigns cname as the name of the specified color. It can be used to define a new color name or redefine an existing one. Color names must begin with an alphabetical letter and may contain only lowercase letters, numbers, hyphens, underscores, and spaces. If cname has embedded spaces, it must be enclosed in quotation marks.

color name tpurple 60,0,80,50
color name tgreen rgba(0%, 80%, 40%, 0.5)

The command color delete can be used to “forget” a specific user-defined color or all custom (user-defined) colors. A built-in color name cannot be deleted.

The command color list lists color names along with color swatches in the Log, with options:

The command “color show cname” reports in the Log the rgba (red, green, blue, opacity) definition of an existing color named cname. See also: palette list

UCSF Resource for Biocomputing, Visualization, and Informatics / October 2017