Built-in coloring schemes are shown below. See also: color, rainbow, palettes, automatic styling, presets
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 colors for volume data
(density maps, etc.) can be customized from the factory defaults of
with the
initialColors option of
volume and
volume defaultvalues.
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:
| Ala | Arg | Asn | Asp | Cys | Gln | Glu | Gly | His | Ile | Leu | Lys | Met | Phe | Pro | Ser | Thr | Trp | Tyr | Val | Asx | Glx | other |
| Ala | Arg | Asn | Asp | Cys | Gln | Glu | Gly | His | Ile | Leu | Lys | Met | Phe | Pro | Ser | Thr | Trp | Tyr | Val | other |
| Ala | Arg | Asn | Asp | Cys | Gln | Glu | Gly | His | Ile | Leu | Lys | Met | Phe | Pro | Ser | Thr | Trp | Tyr | Val |
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 |
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