Command-Line Color Specification

Colors can be specified in commands (color, etc.) with:

predefined color names
color names defined by the user with color name
hexadecimal format starting with # and encoding rgb (3, 6, or 12 digits) or rgba (4, 8, or 16 digits), for example: #00ced1
rgb or rgba given as three or four comma-separated values in the range 0-100 (no spaces, no % signs), for example: 75,10,55
CSS-like specifications in the following formats:
- rgb(red, green, blue)
- rgba(red, green, blue, alpha)
- hsl(hue, saturation, lightness)
- hsla(hue, saturation, lightness, alpha)
- gray(grayscale)
The colorspace name must be in lowercase and immediately precede the open parenthesis. Otherwise, embedded spaces are allowed. Values for red, green, blue, alpha (increasing transparent → opaque), saturation, lightness, and grayscale (increasing black → white) can be given as:
- percentages indicated with %
- fractional values in the range 0-1, indicated with a decimal point (for example, 1. rather than 1)
The red, green, blue, and grayscale components can also be expressed as whole numbers in the range 0-255. Values for hue are in the range 0-360, corresponding to angular positions on the color wheel. See more examples.

The command color list lists the available names along with color swatches in the Log. Color names can be truncated, with ambiguous truncations going to the shortest of the matching full names. See also: color schemes, palettes, command usage conventions, limitations of transparency

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Color Names

The following color names (X11 colors from the CSS3 specification) are predefined in ChimeraX. Color names can be truncated, but they must be entered in lowercase only. The spaces in multiword names are optional, and “grey” may be substituted for “gray.” More names can be defined with the command color name. See also: Color Actions, the Actions... Color menu

Name	Hex	RGB (%)
misty rose	`#FFE4E1`	100,89,88
pink	`#FFC0CB`	100,75,80
light pink	`#FFB6C1`	100,71,76
hot pink	`#FF69B4`	100,41,71
deep pink	`#FF1493`	100,8,58
medium violet red	`#C71585`	78,8,52
pale violet red	`#DB7093`	86,44,58
light coral	`#F08080`	94,50,50
salmon	`#FA8072`	98,50,45
light salmon	`#FFA07A`	100,63,48
dark salmon	`#E9967A`	91,59,48
indian red	`#CD5C5C`	80,36,36
crimson	`#DC143C`	86,8,24
firebrick	`#B22222`	70,13,13
brown	`#A52A2A`	65,17,17
dark red	`#8B0000`	54,0,0
maroon	`#800000`	50,0,0
red	`#FF0000`	100,0,0
orange red	`#FF4500`	100,27,0
tomato	`#FF6347`	100,39,28
coral	`#FF7F50`	100,50,31
dark orange	`#FF8C00`	100,55,0
orange	`#FFA500`	100,65,0
gold	`#FFD700`	100,84,0
yellow	`#FFFF00`	100,100,0
khaki	`#F0E68C`	94,90,55
goldenrod	`#DAA520`	86,65,12
dark goldenrod	`#B8860B`	72,52,4
lemon chiffon	`#FFFACD`	100,98,80
light goldenrod yellow	`#FAFAD2`	98,98,82
light yellow	`#FFFFE0`	100,100,88
cornsilk	`#FFF8DC`	100,97,86
papaya whip	`#FFEFD5`	100,94,84
blanched almond	`#FFEBCD`	100,92,80
peach puff	`#FFDAB9`	100,86,72
bisque	`#FFE4C4`	100,89,77
moccasin	`#FFE4B5`	100,89,71
navajo white	`#FFDEAD`	100,87,68
wheat	`#F5DEB3`	96,87,70
burly wood	`#DEB887`	87,72,53
tan	`#D2B48C`	82,71,55
sandy brown	`#F4A460`	96,64,38
peru	`#CD853F`	80,52,25
chocolate	`#D2691E`	82,41,12
saddle brown	`#8B4513`	54,27,8
sienna	`#A0522D`	63,32,18
rosy brown	`#BC8F8F`	74,56,56

Name	Hex	RGB (%)
beige	`#F5F5DC`	96,96,86
pale goldenrod	`#EEE8AA`	93,91,67
dark khaki	`#BDB76B`	74,72,42
dark olive green	`#556B2F`	33,42,18
olive	`#808000`	50,50,0
olive drab	`#6B8E23`	42,56,14
yellow green	`#9ACD32`	60,80,20
green yellow	`#ADFF2F`	68,100,18
chartreuse	`#7FFF00`	50,100,0
lawn green	`#7CFC00`	49,99,0
lime	`#00FF00`	0,100,0
lime green	`#32CD32`	20,80,20
forest green	`#228B22`	13,54,13
green	`#008000`	0,50,0
dark green	`#006400`	0,39,0
pale green	`#98FB98`	60,98,60
light green	`#90EE90`	56,93,56
spring green	`#00FF7F`	0,100,50
medium spring green	`#00FA9A`	0,98,60
medium sea green	`#3CB371`	24,70,44
sea green	`#2E8B57`	18,54,34
dark sea green	`#8FBC8F`	56,74,56
medium aquamarine	`#66CDAA`	40,80,67
aquamarine	`#7FFFD4`	50,100,83
turquoise	`#40E0D0`	25,88,82
medium turquoise	`#48D1CC`	28,82,80
light sea green	`#20B2AA`	12,70,67
cyan (aqua)	`#00FFFF`	0,100,100
dark turquoise	`#00CED1`	0,81,82
cadet blue	`#5F9EA0`	34,62,63
dark cyan	`#008B8B`	0,54,54
teal	`#008080`	0,50,50
pale turquoise	`#AFEEEE`	69,93,93
powder blue	`#B0E0E6`	69,88,90
light blue	`#ADD8E6`	68,85,90
light steel blue	`#B0C4DE`	69,77,87
steel blue	`#4682B4`	28,51,71
sky blue	`#87CEEB`	53,81,92
light sky blue	`#87CEFA`	53,81,98
deep sky blue	`#00BFFF`	0,75,100
dodger blue	`#1E90FF`	12,56,100
cornflower blue	`#6495ED`	39,58,93
royal blue	`#4169E1`	26,41,88
blue	`#0000FF`	0,0,100
medium blue	`#0000CD`	0,0,80
dark blue	`#00008B`	0,0,54
navy	`#000080`	0,0,50

Name	Hex	RGB (%)
lavender	`#E6E6FA`	90,90,98
thistle	`#D8BFD8`	85,75,85
plum	`#DDA0DD`	87,63,87
violet	`#EE82EE`	93,51,93
orchid	`#DA70D6`	86,44,84
magenta (fuchsia)	`#FF00FF`	100,0,100
dark magenta	`#8B008B`	54,0,54
purple	`#800080`	50,0,50
medium orchid	`#BA55D3`	73,33,83
dark orchid	`#9932CC`	60,20,80
dark violet	`#9400D3`	58,0,83
blue violet	`#8A2BE2`	54,17,89
medium purple	`#9370DB`	58,44,86
rebecca purple	`#663399`	40,20,60
indigo	`#4B0082`	29,0,51
medium slate blue	`#7B68EE`	48,41,93
slate blue	`#6A5ACD`	42,35,80
dark slate blue	`#483D8B`	28,24,54
midnight blue	`#191970`	10,10,44
white	`#FFFFFF`	100,100,100
snow	`#FFFAFA`	100,98,98
mint cream	`#F5FFFA`	96,100,98
honeydew	`#F0FFF0`	94,100,94
azure	`#F0FFFF`	94,100,100
light cyan	`#E0FFFF`	88,100,100
alice blue	`#F0F8FF`	94,97,100
ghost white	`#F8F8FF`	97,97,100
white smoke	`#F5F5F5`	96,96,96
lavender blush	`#FFF0F5`	100,94,96
seashell	`#FFF5EE`	100,96,93
old lace	`#FDF5E6`	99,96,90
floral white	`#FFFAF0`	100,98,94
ivory	`#FFFFF0`	100,100,94
linen	`#FAF0E6`	98,94,90
antique white	`#FAEBD7`	98,92,84
gainsboro	`#DCDCDC`	86,86,86
light gray	`#D3D3D3`	83,83,83
silver	`#C0C0C0`	75,75,75
dark gray	`#A9A9A9`	66,66,66
gray	`#808080`	50,50,50
dim gray	`#696969`	41,41,41
light slate gray	`#778899`	47,53,60
slate gray	`#708090`	44,50,56
dark slate gray	`#2F4F4F`	18,31,31
black	`#000000`	0,0,0

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More Examples

The following all specify the same color:

red
#f00
#FF0000FF
100,0,0
100,0,0,100
rgb(255, 0, 0)
rgb(1., 0., 0.)
rgb(100%, 0%, 0%)
rgba(100%, 0%, 0%, 1)
rgba(100%, 0%, 0%, 100%)
hsl(0, 1.0, 0.5)
hsl(0, 100%, 50%)

The following specify the same shade of gray:

gray(128)
gray(50%)

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Transparency and Its Limitations

Objects can be made transparent by including transparency (alpha < 100%) in command-line color specifications. In addition, the transparency command or the color command transparency option can be used, as well as the system color-editing dialog (e.g., shown by using menu: Actions... Color... From Editor).

Unfortunately, ChimeraX does not correctly render transparency when there are multiple transparent models, with the exception of multichannel volume data rendered in the image display style.

As in Chimera, ChimeraX does not correctly render the transparency of multiple models because it draws one model at a time and only keeps track of the front-most as drawing occurs. When more than one model is transparent, ChimeraX shows only the frontmost transparent model at each pixel position. Any transparent models that are behind another transparent model will simply be invisible. An alternative to transparency for surfaces is to show them in the mesh style. Since rendering is correct for opaque models behind transparent ones, another possibility is to make only the outermost surface transparent, keeping inner objects opaque.

UCSF Resource for Biocomputing, Visualization, and Informatics / May 2021