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, measure convexity, surface, volume, Basic Actions, Molecule Display Toolbar, initial colors, color names, palettes
Additional subcommands manage the set of named colors:
Usage: color spec colorname [ target string ] [ halfbond true | false ] [ transparency percent ]
Simple coloring applies to atomic models, including cartoon and molecular surface representations, and volume data (map) displays. The colorname can be:
The target option allows 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:
Alternatively, for simple coloring only, targets can be specified with one or more of the following keywords as a comma-separated list immediately after the colorname (or for color modification, at the end of the command):
The transparency option sets 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.
Usage: color sequential atom-spec [ level ] [ target string ] [ palette palette ] [ transparency percent ]
– or –
Usage: rainbow atom-spec [ level ] [ target string ] [ palette palette ] [ transparency percent ]
The color sequential command (synonym rainbow, see examples) applies a series of colors to atomic models at the specified level:
Usage: color modify spec hue [ + | − ] angle [ target string ]
Usage: color modify spec ( saturation | lightness | whiteness | blackness | red | green | blue ) [ + | − | * ] percent [ target string ]
Usage: color modify spec contrast [ percent ] [ target string ]
Color modification adjusts existing colors. It applies to atomic models, including cartoon and molecular surface representations. The color component to modify must be specified, with choices:
For saturation, lightness, whiteness, blackness, red, green, or blue, the percent can be added to (+), subtracted from (−), or multiplied by (*) the current value, or simply set as the current value if no operator symbol is given (or the space after the operator symbol is omitted; the space is needed to indicate a change from the current value rather than an absolute value). For hue, the angle can be added to or subtracted from the current value, or simply set as the current value.
Usage: color ( sample | electrostatic | gradient ) surf-spec map map-model [ offset d ] [ transparency percent ] palette-options
Coloring by map (volume data) value applies to surfaces only, both molecular and nonmolecular. The color-to-value mapping is specified with palette options, and transparency can be set independently. See also: mlp
Usage: color radial surf-spec [ center atom-spec | x,y,z ] [ coordinateSystem model-spec ] palette-options
Usage: color ( cylindrical | height ) surf-spec [ center atom-spec | x,y,z ] [ axis vector ] [ coordinateSystem model-spec ] palette-options
Coloring by distance applies to surfaces only, both molecular and nonmolecular (such as volume isosurfaces). The color-to-distance mapping is specified with palette options.
The axis vector can be expressed as:
Usage: color zone surf-spec near atom-spec [ distance cutoff ] [ sharpEdges true | false ]
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). The sharpEdges option (default false) subdivides surface triangles to create sharp boundaries between the different colored regions.
A palette is an ordered set of colors or value,color pairs used for sequential coloring or coloring by map value. See also: mlp, measure convexity
Specify a palette as one of the following:
- palette-name - the name of an existing palette; the command palette list lists the names of the available palettes in the Log. Predefined palettes include the following, with colors shown in ascending value order:
- rainbow (default for sequential coloring)
- red-white-blue or redblue (default for coloring by map value)
- blue-white-red or bluered
- cyan-white-maroon or cyanmaroon
- cyan-gray-maroon (default for measure convexity, along with range -1,1)
- grayscale or gray
- lipophilicity (default for the mlp command, along with range -20,20)
- ColorBrewer palettes - a default number of colors will be used if the number is omitted from the name. Examples:palette pastel2-4Users should cite: www.ColorBrewer.org, color specifications and designs by Cynthia A. Brewer, Pennsylvania State University.
- color1:color2:color3... a series of color specifications separated by colons, collectively enclosed in quotation marks if it contains any spaces (example: palette cornflowerblue:red:gold or palette "cornflower blue:red:gold"). The colors are placed evenly in ascending value order along the range, with the first and last colors at the extremes. Colors for intermediate values are interpolated.
- value1,color1:value2,color2:value3,color3... a series of value,color pairs separated by colons, collectively enclosed in quotation marks if it contains any spaces (example: palette "0,cornflower blue:1,gold:0.7,red"). For sequential coloring, an entire range (such as the residues in each chain or the chains in each model) is always mapped to fractional values 0.0-1.0. For numerical data, the values can be expressed directly on the scale of the data (range not used) or as fractional values 0.0-1.0 across a range of data specified with range. Values below the lowest given value will map to the same color as the lowest, and values above the highest will map to the same color as the highest. Colors are interpolated between specified value-color pairs; discrete coloring can be achieved by specifying the same color for the upper- and lower-bound values of a “bin.”
- colourlovers-id - the ID number, name, or name+author of a palette to be fetched from COLOURlovers.com. Examples:palette 92095The page of a specific palette at COLOURlovers.com shows its name, author, ID number (in the URL), and any licensing stipulations for its use. Palette names with spaces must be enclosed in quotation marks. Palette names are not necessarily unique, and the most-viewed palette of a specified name will be fetched unless by author is appended, as in the example above. Palette and author names must be capitalized as shown on the website. Palettes with “all rights reserved” cannot be fetched. In ChimeraX, the palette colors are used in left-to-right order, spaced equally along the range of values. Web-fetched palettes are cached locally as described for open.
palette "Giant Goldfish"
palette "Giant Goldfish by manekineko"
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 cColor residues 12 and 260-275 in chains A and B, atoms/bonds only:
– or –
color /d & helix sky blue cartoons
color /A,B:12,260-275 hot pink target aColor all pseudobonds yellow:
– or –
color /A,B:12,260-275 hot pink atoms
color pbonds yellowRestore original model coloring to all carbon atoms:
color C bymodel targ aRainbow-color residues blue → red along each biopolymer chain:
color seq resColor 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):
– or –
– or –
color seq polymers targ c palette cornflowerblue:red:goldColor the protein 10-mer in PDB entry 1qmv using the 10-color version of the “paired” ColorBrewer palette:
– or –
rainbow polymers targ c palette cornflowerblue:red:gold
open 1qmv; rainbow protein chain palette paired-10
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.Examples:
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