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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.

Per-chain molecular surface models are initially colored by 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 

This is also the color command bychain scheme. Unique colors are generated automatically for other chain IDs (for example, those with two characters).

Similarly, there are default initial colors for volume data sets:

Coloring by Residue Type

The color command bynucleotide scheme colors residues by base type as in the Nucleic Acid Database:
A T C G U

A few schemes for coloring proteins by amino acid type are available as ChimeraX command scripts (see comments in the files for details):

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 / January 2018