Colors

Jmol colors

Objects can be custom colored in Jmol using the color (or colour) command:
color [object] [color or color scheme]

Information on RasMol colors is included for those who are adapting RasMol and Chime-based materials for use in Jmol.

Many of the following coloring patterns apply only to PDB and mmCIF files for biomacromolecules.

Atoms ('CPK' colors, default element colors)

Related commands:
color [object] cpk , set defaultColors Jmol , set defaultColors Rasmol

Applies color to each atom of the object according to element, as shown in the tables below. Backbone displays such as ribbons, cartoons, etc. are rendered in the color of alpha carbons for proteins, phosphorus for nucleic acids.

Default element colors, by periodic table:

Hover over any element to see more information.
Click on an element to move to the same information in the Atomic Numbers table below.
HHe
LiBeBCNOFNe
NaMgAlSiPSClAr
KCaScTiVCrMnFeCoNiCuZn GaGeAsSeBrKr
RbSrYZrNbMoTcRuRhPdAgCd InSnSbTeIXe
CsBaL*HfTaWReOsIrPtAuHg TlPbBiPoAtRn
FrRaA*RfDbSgBhHsMt          
 
 (L:)LaCePrNdPmSmEuGd TbDyHoErTmYbLu 
 (A:)AcThPaU NpPuAmCm BkCfEsFmMdNoLr 

Default element colors, by atomic number:

“CPKnew” scheme applies only to Rasmol v. 2.7.3 (or later); only differences with classic CPK are shown. Note: CPKnew for unknown atoms is FA1691, slightly different from CPK FF1493, but has been omitted for clarity in the table.
  Jmol Rasmol Rasmol
“CPKnew”
1H[255,255,255]FFFFFF   FFFFFF     
2He[217,255,255]D9FFFF   FFC0CB     
3Li[204,128,255]CC80FF   B22222   B22121  
4Be[194,255,0]C2FF00   FF1493     
5B[255,181,181]FFB5B5   00FF00     
6C[144,144,144]909090   C8C8C8   D3D3D3  
7N[48,80,248]3050F8   8F8FFF   87CEE6  
8O[255,13,13]FF0D0D   F00000   FF0000  
9F[144,224,80]90E050   DAA520     
10Ne[179,227,245]B3E3F5   FF1493     
11Na[171,92,242]AB5CF2   0000FF     
12Mg[138,255,0]8AFF00   228B22     
13Al[191,166,166]BFA6A6   808090   696969  
14Si[240,200,160]F0C8A0   DAA520     
15P[255,128,0]FF8000   FFA500   FFAA00  
16S[255,255,48]FFFF30   FFC832   FFFF00  
17Cl[31,240,31]1FF01F   00FF00     
18Ar[128,209,227]80D1E3   FF1493     
19K[143,64,212]8F40D4   FF1493     
20Ca[61,255,0]3DFF00   808090   696969  
21Sc[230,230,230]E6E6E6   FF1493     
22Ti[191,194,199]BFC2C7   808090   696969  
23V[166,166,171]A6A6AB   FF1493     
24Cr[138,153,199]8A99C7   808090   696969  
25Mn[156,122,199]9C7AC7   808090   696969  
26Fe[224,102,51]E06633   FFA500   FFAA00  
27Co[240,144,160]F090A0   FF1493     
28Ni[80,208,80]50D050   A52A2A   802828  
29Cu[200,128,51]C88033   A52A2A   802828  
30Zn[125,128,176]7D80B0   A52A2A   802828  
31Ga[194,143,143]C28F8F   FF1493     
32Ge[102,143,143]668F8F   FF1493     
33As[189,128,227]BD80E3   FF1493     
34Se[255,161,0]FFA100   FF1493     
35Br[166,41,41]A62929   A52A2A   802828  
36Kr[92,184,209]5CB8D1   FF1493     
37Rb[112,46,176]702EB0   FF1493     
38Sr[0,255,0]00FF00   FF1493     
39Y[148,255,255]94FFFF   FF1493     
40Zr[148,224,224]94E0E0   FF1493     
41Nb[115,194,201]73C2C9   FF1493     
42Mo[84,181,181]54B5B5   FF1493     
43Tc[59,158,158]3B9E9E   FF1493     
44Ru[36,143,143]248F8F   FF1493     
45Rh[10,125,140]0A7D8C   FF1493     
46Pd[0,105,133]006985   FF1493     
47Ag[192,192,192]C0C0C0   808090   696969  
48Cd[255,217,143]FFD98F   FF1493     
49In[166,117,115]A67573   FF1493     
50Sn[102,128,128]668080   FF1493     
51Sb[158,99,181]9E63B5   FF1493     
52Te[212,122,0]D47A00   FF1493     
53I[148,0,148]940094   A020F0     
54Xe[66,158,176]429EB0   FF1493     
55Cs[87,23,143]57178F   FF1493     
56Ba[0,201,0]00C900   FFA500   FFAA00  
57La[112,212,255]70D4FF   FF1493     
58Ce[255,255,199]FFFFC7   FF1493     
59Pr[217,255,199]D9FFC7   FF1493     
60Nd[199,255,199]C7FFC7   FF1493     
61Pm[163,255,199]A3FFC7   FF1493     
62Sm[143,255,199]8FFFC7   FF1493     
63Eu[97,255,199]61FFC7   FF1493     
64Gd[69,255,199]45FFC7   FF1493     
65Tb[48,255,199]30FFC7   FF1493     
66Dy[31,255,199]1FFFC7   FF1493     
67Ho[0,255,156]00FF9C   FF1493     
68Er[0,230,117]00E675   FF1493     
69Tm[0,212,82]00D452   FF1493     
70Yb[0,191,56]00BF38   FF1493     
71Lu[0,171,36]00AB24   FF1493     
72Hf[77,194,255]4DC2FF   FF1493     
73Ta[77,166,255]4DA6FF   FF1493     
74W[33,148,214]2194D6   FF1493     
75Re[38,125,171]267DAB   FF1493     
76Os[38,102,150]266696   FF1493     
77Ir[23,84,135]175487   FF1493     
78Pt[208,208,224]D0D0E0   FF1493     
79Au[255,209,35]FFD123   DAA520     
80Hg[184,184,208]B8B8D0   FF1493     
81Tl[166,84,77]A6544D   FF1493     
82Pb[87,89,97]575961   FF1493     
83Bi[158,79,181]9E4FB5   FF1493     
84Po[171,92,0]AB5C00   FF1493     
85At[117,79,69]754F45   FF1493     
86Rn[66,130,150]428296   FF1493     
87Fr[66,0,102]420066   FF1493     
88Ra[0,125,0]007D00   FF1493     
89Ac[112,171,250]70ABFA   FF1493     
90Th[0,186,255]00BAFF   FF1493     
91Pa[0,161,255]00A1FF   FF1493     
92U[0,143,255]008FFF   FF1493     
93Np[0,128,255]0080FF   FF1493     
94Pu[0,107,255]006BFF   FF1493     
95Am[84,92,242]545CF2   FF1493     
96Cm[120,92,227]785CE3   FF1493     
97Bk[138,79,227]8A4FE3   FF1493     
98Cf[161,54,212]A136D4   FF1493     
99Es[179,31,212]B31FD4   FF1493     
100Fm[179,31,186]B31FBA   FF1493     
101Md[179,13,166]B30DA6   FF1493     
102No[189,13,135]BD0D87   FF1493     
103Lr[199,0,102]C70066   FF1493     
104Rf[204,0,89]CC0059   FF1493     
105Db[209,0,79]D1004F   FF1493     
106Sg[217,0,69]D90045   FF1493     
107Bh[224,0,56]E00038   FF1493     
108Hs[230,0,46]E6002E   FF1493     
109Mt[235,0,38]EB0026   FF1493     
  
 
Jmol
1D,2H[255,255,192]FFFFC0  
1T,3H[255,255,160]FFFFA0  
613C[80,80,80]505050  
614C[64,64,64]404040  
715N[16,80,80]105050  

Residues: amino acids, nucleotides

Related commands: color [object] amino, color [object] shapely

'amino' renders each of the 20 standard amino acid residues (as well as Asx and Glx) in a certain color, along with one additional color for anything else (including nucleotides, solvents, and non-amino ligands). Some colors are shared by two or more amino acids with similar properties.

'shapely' uses a different set of colors for amino acids (each one different) and also colors differentially the 6 kinds of nucleotides.

 Protein
“amino”
  Protein
“shapely”
Ala[200,200,200]C8C8C8   [140,255,140]8CFF8C  
Arg[20,90,255]145AFF   [0,0,124]00007C  
Asn[0,220,220]00DCDC   [255,124,112]FF7C70  
Asp[230,10,10]E60A0A   [160,0,66]A00042  
Cys[230,230,0]E6E600   [255,255,112]FFFF70  
Gln[0,220,220]00DCDC   [255,76,76]FF4C4C  
Glu[230,10,10]E60A0A   [102,0,0]660000  
Gly[235,235,235]EBEBEB   [255,255,255]FFFFFF  
His[130,130,210]8282D2   [112,112,255]7070FF  
Ile[15,130,15]0F820F   [0,76,0]004C00  
Leu[15,130,15]0F820F   [69,94,69]455E45  
Lys[20,90,255]145AFF   [71,71,184]4747B8  
Met[230,230,0]E6E600   [184,160,66]B8A042  
Phe[50,50,170]3232AA   [83,76,82]534C52  
Pro[220,150,130]DC9682   [82,82,82]525252  
Ser[250,150,0]FA9600   [255,112,66]FF7042  
Thr[250,150,0]FA9600   [184,76,0]B84C00  
Trp[180,90,180]B45AB4   [79,70,0]4F4600  
Tyr[50,50,170]3232AA   [140,112,76]8C704C  
Val[15,130,15]0F820F   [255,140,255]FF8CFF  
Asx[255,105,180]FF69B4   [255,0,255]FF00FF  
Glx[255,105,180]FF69B4   [255,0,255]FF00FF  
other[190,160,110]BEA06E   [255,0,255]FF00FF  
(same in RasMol, except amino for other)
 
 Nucleic
“shapely”
A[160,160,255]A0A0FF  
G[255,112,112]FF7070  
I[128,255,255]80FFFF  
C[255,140,75]FF8C4B  
T[160,255,160]A0FFA0  
U[255,128,128]FF8080  
(A,G,C,T same in RasMol)

Chains

Related command: color [object] chain

Renders each chain in the structure in a different color. This color scheme is particularly useful for distinguishing the parts of a multimeric structure or the individual DNA strands of a double helix. Atoms in HETERO groups (PDB files only) are colored in a different shade than those in ATOM records: darker for chains A-Q,S, lighter for chains R,T-Z.

The PDB format requires that each chain ID be a non-blank alphanumeric character. Thus, a maximum of 62 chains is permitted in a single model within a PDB file (26 times 2, for upper and lower case letters A-Z, plus 10, for chain IDs 0-9). An example with 62 chains is 2zkr. PDB files obtained before remediation of the database may have chain IDs that are blank or not alphanumeric (e.g. punctuation characters) but this is no longer permitted. Although chain 'A' is the same color as chain 'a' (and so forth), they may be selected independently (see the set chainCaseSensitive command).

Chain
ID
ATOM HETATM
A, a[192,208,255]C0D0FF   [144,160,207]90A0CF  
B, b[176,255,176]B0FFB0   [128,207,152]80CF98  
C, c[255,192,200]FFC0C8   [207,144,176]CF90B0  
D, d[255,255,128]FFFF80   [207,207,112]CFCF70  
E, e[255,192,255]FFC0FF   [207,144,207]CF90CF  
F, f[176,240,240]B0F0F0   [128,192,192]80C0C0  
G, g[255,208,112]FFD070   [207,160,96]CFA060  
H, h[240,128,128]F08080   [192,80,112]C05070  
I, h[245,222,179]F5DEB3   [197,174,131]C5AE83  
J, j[0,191,255]00BFFF   [0,167,207]00A7CF  
K, k[205,92,92]CD5C5C   [181,76,76]B54C4C  
L, l[102,205,170]66CDAA   [86,181,146]56B592  
M, m[154,205,50]9ACD32   [138,181,42]8AB52A  
N, n[238,130,238]EE82EE   [190,114,190]BE72BE  
O, o[0,206,209]00CED1   [0,182,161]00B6A1  
P, p, 0[0,255,127]00FF7F   [0,207,111]00CF6F  
Q, q, 1[60,179,113]3CB371   [52,155,97]349B61  
R, r, 2[0,0,139]00008B   [0,0,187]0000BB  
S, s, 3[189,183,107]BDB76B   [165,159,91]A59F5B  
T, t, 4[0,100,0]006400   [0,148,0]009400  
U, u, 5[128,0,0]800000   [176,0,0]B00000  
V, v, 6[128,128,0]808000   [176,176,0]B0B000  
W, w, 7[128,0,128]800080   [176,0,176]B000B0  
X, x, 8[0,128,128]008080   [0,176,176]00B0B0  
Y, y, 9[184,134,11]B8860B   [232,182,19]E8B613  
Z, z[178,34,34]B22222   [194,50,50]C23232  
none[255,255,255]FFFFFF   [255,255,255]FFFFFF  

Secondary structure

Related command: color [object] structure

Uses different colors to distinguish six types of protein secondary structures (three types of helices, beta strands or sheets, turns, and loops) and DNA vs. RNA. The secondary structure is either read from the PDB file (HELIX and SHEET records), if available, or determined using an algorithm.

Protein
α helix[255,0,128]FF0080  
310 helix[160,0,128]A00080  
π helix[96,0,128]600080  
β strand[255,200,0]FFC800  
(β) turn[96,128,255]6080FF  
other[255,255,255]FFFFFF  
(same in RasMol, except 310 and π)
 
Nucleic acid
DNA[174,0,254]AE00FE  
RNA[253,1,98]FD0162  
(same in DRuMS)
 
Other
carbohydrate[166,166,250]A6A6FA  
other[128,128,128]808080  

Gradients

Several properties that adopt a continuous range of values can be used to color atoms and structures. In these cases, several color gradients or "rainbows" are used by Jmol.

Direct rainbow (roygb)

red -> orange -> yellow -> green -> blue

Reverse rainbow (bgyor)

blue -> green -> yellow -> orange -> red

Red-white-blue gradient (rwb)

red -> tints of red-pink -> white -> tints of blue -> blue

Blue-white-red gradient (bwr)

blue -> tints of blue -> white -> tints of pink-red -> red

Low rainbow

red -> orange -> yellow

High rainbow

yellow -> green -> blue

Position along chain

Related commands: color [object] group, color [object] monomer

A reverse rainbow gradient (bgyor) is used to color according to position of the corresponding groups or residues (for example, amino acids or nucleotides) along a chain.

N-terminal or 5’- C-terminal or 3’-
                                                                  

(blue = nitrogen = N-terminal = start of chain = 5')
(red = oxygen = C-terminal = end of chain = 3')

'group':

'monomer':

A variation, relating to "monomers" in a "polymer" rather than "groups" in a "chain". A "polymer" is a series of connected "monomers" (at least for these purposes).

RasMol/Chime note: In RasMol/Chime, group index is relative to the full chain, while in Jmol it is relative to the currently selected groups of the chain. In addition, the "set hetero" command is not implemented in Jmol. If you want to exclude "hetero" groups, then do not select them.

Positional Variability

Related commands: color [object] relativeTemperature, color [object] fixedTemperature

Colors each atom, using a bwr gradient, according to the "temperature factor" (B factor, or Debye-Waller factor) value stored in the PDB or mmCIF file. Typically this gives a measure of the mobility or uncertainty of a given atom's position. A high crystallographic B factor may indicate an incorrect structure.

lowest positional variability highest positional variability
                                                              

(blue = cold = low temperature = static/immobile)
(red = hot = high temperature = variable/mobile)

'fixedTemperature': the factor is referred to an absolute scale of 0 to 100.

'relativeTemperature': the color is relative to the lowest and highest B factor values within the file (not within the selection).

'relativeTemperature' after 'set rangeSelected on': the color is relative to the lowest and highest B factor values within the currently selected part of the model.

Note: The temperature factor fields in a PDB file are sometimes used by the file creator to indicate any other characteristic of the atoms in the model.

RasMol/Chime note: In RasMol and Chime, 'temperature' (the only option available) uses also a relative scale, but with a reverse rainbow gradient (bgyor). In Jmol, 'temperature' does the same as 'relativeTemperature'.

Charge

Formal charge

Related command: color [object] formalCharge

Colors atoms based on their formal charge, or ionic state. Uses a restricted rwb gradient: tints of red for anions, tints of blue for cations, white for uncharged atoms. The range of values handled by Jmol for formal charge is -4 through +7, in an absolute scale.

Charge 
-4[255,0,0]FF0000  
-3[255,64,64]FF4040  
-2[255,128,128]FF8080  
-1[255,192,192]FFC0C0  
0[255,255,255]FFFFFF  
1[216,216,255]D8D8FF  
2[180,180,255]B4B4FF  
3[144,144,255]9090FF  
4[108,108,255]6C6CFF  
5[72,72,255]4848FF  
6[36,36,255]2424FF  
7[0,0,255]0000FF  

(red = oxygen = carboxy = negative)
(blue = nitrogen = amino = positive)

Partial charge

Related command: color [object] partialCharge

Colors atoms based on their partial charge, or electron density. Uses a rwb gradient: tints of red for high electron density, tints of blue for low electron density, white for neutral. The range of values for partial charge is adjusted to the minimum and maximum values present in the file (i.e., a scale relative to the file values is used, but not to values in the selected set of atoms).

negative charge positive charge
                                                              

(red = oxygen = carboxy = negative)
(blue = nitrogen = amino = positive)

RasMol/Chime note: In RasMol and Chime, 'charge' (the only option available) is meant for PDB files that hold partial charges in the B factor columns, and uses a direct rainbow gradient (roygb) with a scale relative to values present in file. In Jmol, 'charge' does the same as 'formalCharge'.

Isosurfaces

Related command: isoSurface

Isosurfaces (solvent, molecular, orbitals...) can be colored uniformly or using a color map that reflects the value of some property at each point in the surface (such as molecular electrostatic potential, distance, etc.). For these maps all the predefined gradients of color are available (and the reverse gradients too), using the 'colorScheme' parameter of 'isoSurface' command.

Hydrogen bonds

Related command: color hBonds type

Colors hydrogen bonds in a protein based on the number of residues between the atoms participating in the bond. A different color is used for hydrogen bonds in nucleic acids.

Distance 
+2FFFFFF  
+3 (turns)FF00FF  
+4 (α-helix)FF0000  
+5FFA500  
-300FFFF  
-400FF00  
other (β-sheet)FFFF00  
base pairsFF8080  

Sources

JavaScript colors

aliceblue #F0F8FF antiquewhite #FAEBD7 aqua #00FFFF aquamarine #7FFFD4 azure #F0FFFF 
beige #F5F5DC bisque #FFE4C4 black #000000 blanchedalmond #FFEBCD blue #0000FF 
blueviolet #8A2BE2 brown #A52A2A burlywood #DEB887 cadetblue #5F9EA0 chartreuse #7FFF00 
chocolate #D2691E coral #FF7F50 cornflowerblue #6495ED cornsilk #FFF8DC crimson #DC143C 
cyan #00FFFF darkblue #00008B darkcyan #008B8B darkgoldenrod #B8860B darkgray #A9A9A9 
darkgreen #006400 darkkhaki #BDB76B darkmagenta #8B008B darkolivegreen #556B2F darkorange #FF8C00 
darkorchid #9932CC darkred #8B0000 darksalmon #E9967A darkseagreen #8FBC8F darkslateblue #483D8B 
darkslategray #2F4F4F darkturquoise #00CED1 darkviolet #9400D3 deeppink #FF1493 deepskyblue #00BFFF 
dimgray #696969 dodgerblue #1E90FF firebrick #B22222 floralwhite #FFFAF0 forestgreen #228B22 
fuchsia #FF00FF gainsboro #DCDCDC ghostwhite #F8F8FF gold #FFD700 goldenrod #DAA520 
gray #808080 green #008000 greenyellow #ADFF2F honeydew #F0FFF0 hotpink #FF69B4 
indianred #CD5C5C indigo #4B0082 ivory #FFFFF0 khaki #F0E68C lavender #E6E6FA 
lavenderblush #FFF0F5 lawngreen #7CFC00 lemonchiffon #FFFACD lightblue #ADD8E6 lightcoral #F08080 
lightcyan #E0FFFF lightgoldenrodyellow #FAFAD2 lightgreen #90EE90 lightgrey #D3D3D3 lightpink #FFB6C1 
lightsalmon #FFA07A lightseagreen #20B2AA lightskyblue #87CEFA lightslategray #778899 lightsteelblue #B0C4DE 
lightyellow #FFFFE0 lime #00FF00 limegreen #32CD32 linen #FAF0E6 magenta #FF00FF 
maroon #800000 mediumaquamarine #66CDAA mediumblue #0000CD mediumorchid #BA55D3 mediumpurple #9370DB 
mediumseagreen #3CB371 mediumslateblue #7B68EE mediumspringgreen #00FA9A mediumturquoise #48D1CC mediumvioletred #C71585 
midnightblue #191970 mintcream #F5FFFA mistyrose #FFE4E1 moccasin #FFE4B5 navajowhite #FFDEAD 
navy #000080 oldlace #FDF5E6 olive #808000 olivedrab #6B8E23 orange #FFA500 
orangered #FF4500 orchid #DA70D6 palegoldenrod #EEE8AA palegreen #98FB98 paleturquoise #AFEEEE 
palevioletred #DB7093 papayawhip #FFEFD5 peachpuff #FFDAB9 peru #CD853F pink #FFC0CB 
plum #DDA0DD powderblue #B0E0E6 purple #800080 red #FF0000 rosybrown #BC8F8F 
royalblue #4169E1 saddlebrown #8B4513 salmon #FA8072 sandybrown #F4A460 seagreen #2E8B57 
seashell #FFF5EE sienna #A0522D silver #C0C0C0 skyblue #87CEEB slateblue #6A5ACD 
slategray #708090 snow #FFFAFA springgreen #00FF7F steelblue #4682B4 tan #D2B48C 
teal #008080 thistle #D8BFD8 tomato #FF6347 turquoise #40E0D0 violet #EE82EE 
wheat #F5DEB3 white #FFFFFF whitesmoke #F5F5F5 yellow #FFFF00 yellowgreen #9ACD32 

Netscape 8 bit color palette

Web Color Chart
by Tony Awtrey
#000000 #101010 #202020 #303030 #404040 
#505050 #606060 #707070 #808080 #909090 #A0A0A0 
#B0B0B0 #C0C0C0 #D0D0D0 #E0E0E0 #F0F0F0 #FFFFFF 
#000000 #003300 #006600 #009900 #00CC00 #00FF00 
#000033 #003333 #006633 #009933 #00CC33 #00FF33 
#000066 #003366 #006666 #009966 #00CC66 #00FF66 
#000099 #003399 #006699 #009999 #00CC99 #00FF99 
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