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Coloring by Model, Chain, Residue, Element

Built-in coloring schemes are shown below. See also: color, rainbow, palettes, automatic styling, presets

Coloring by Model or Chain (Initial Colors)

Default initial colors for atomic models are tan, sky blue, plum, light green, salmon, light gray, deep pink, gold, dodger blue and purple (see color names):

 #1   #2   #3   #4   #5   #6   #7   #8   #9   #10 

This is also the color command bymodel scheme. If any of the colors would exactly match the background, a different model color is used instead. For higher model numbers, an algorithm is used to produce colors distinguishable from the background and from other models.

Metal-coordination pseudobonds are shown in medium purple
.

Coloring by chain (as with the color command bychain scheme) is based on chain ID, for example:

 A,a   B,b   C,c   D,d   E,e   F,f   G,g   H,h   I,i   J,j   K,k   L,l   M,m   N,n   O,o   P,p   Q,q   R,r 
 S,s   T,t   U,u   V,v   W,w   X,x   Y,y   Z,z   1   2   3   4   5   6   7   8   9   0 

Unique colors are generated automatically for other chain IDs, such as those with two characters. See also the color command bypolymer coloring.

Initial Map Colors

Initial colors for volume data (density maps, etc.) can be customized from the factory defaults of with the initialColors option of volume and volume defaultvalues.

Coloring by Residue Type

The color command bynucleotide scheme colors residues by nucleotide base type:
A T G C U P I

A few schemes for coloring proteins by amino acid type are available as ChimeraX command scripts (see comments in the files for details) that could be run directly or used to make a custom preset:

Element Colors

The color command byelement and byhet schemes use the Jmol default element colors. Pausing the cursor over a cell in the table below shows the corresponding hexadecimal color code.

1
H
2
He
3
Li
4
Be
5
B
6
C
7
N
8
O
9
F
10
Ne
11
Na
12
Mg
13
Al
14
Si
15
P
16
S
17
Cl
18
Ar
19
K
20
Ca
21
Sc
22
Ti
23
V
24
Cr
25
Mn
26
Fe
27
Co
28
Ni
29
Cu
30
Zn
31
Ga
32
Ge
33
As
34
Se
35
Br
36
Kr
37
Rb
38
Sr
39
Y
40
Zr
41
Nb
42
Mo
43
Tc
44
Ru
45
Rh
46
Pd
47
Ag
48
Cd
49
In
50
Sn
51
Sb
52
Te
53
I
54
Xe
55
Cs
56
Ba
(L) 72
Hf
73
Ta
74
W
75
Re
76
Os
77
Ir
78
Pt
79
Au
80
Hg
81
Tl
82
Pb
83
Bi
84
Po
85
At
86
Rn
87
Fr
88
Ra
(A) 104
Rf
105
Db
106
Sg
107
Bh
108
Hs
109
Mt
 
L: 57
La
58
Ce
59
Pr
60
Nd
61
Pm
62
Sm
63
Eu
64
Gd
65
Tb
66
Dy
67
Ho
68
Er
69
Tm
70
Yb
71
Lu
A: 89
Ac
90
Th
91
Pa
92
U
93
Np
94
Pu
95
Am
96
Cm
97
Bk
98
Cf
99
Es
100
Fm
101
Md
102
No
103
Lr

UCSF Resource for Biocomputing, Visualization, and Informatics / November 2023