Objects can be custom colored in Jmol using the color (or colour) command:
color [object] [color or color scheme]
- [color] is specified as decimal [red,green,blue] or hexadecimal [xRRGGBB] triplets. It can also be a JavaScript color name, a RasMol color name, or a Jmol color name. (For the default colors and color values used in Jmol, see tables below.)
- [color scheme] is specified using pre-defined terms detailed on this page.
- [object] can be atoms, bonds, backbone, cartoon, stars, rockets, ribbon, dots, label, echo, hbonds, ssbonds, axes, boundbox, measures, polyhedra, isosurface, pmesh, unitcell.
- if the object is omitted, atoms is assumed
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 RasmolApplies 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.
H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba L* Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Fr Ra A* Rf Db Sg Bh Hs Mt (L:) La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu (A:) Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr 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.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.
(same in RasMol, except amino for other)
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 (A,G,C,T same in RasMol)
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 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
IDATOM 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.
(same in RasMol, except 310 and π)
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 DRuMS)
Nucleic acid DNA [174,0,254] AE00FE RNA [253,1,98] FD0162
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 rainbowred -> orange -> yellow
High rainbowyellow -> 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':
- The full color range is applied across the specified or selected groups in the chain (that is, the scale is relative, not absolute).
- The order of groups in the file is used, not the number assigned to them in the file.
- The coloring operates independently for each chain.
'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).
- Jmol interprets the backbone pattern of consecutive residues ("monomers") to identify continuous "polymers".
- If a chain has a break in it, the 2 pieces of the chain are recognized as separate polymers, and hence each one is colored independently with the full color range, despite the fact that both parts are designated with the same chain ID in the coordinate file.
- Again, the numbering of groups in the file is irrelevant.
- HETERO groups may participate in a polymer, depending upon how the PDB/mmCIF file is marked up, and as long as they have a backbone pattern that Jmol can recognize as a sequence of individual units.
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 +2 FFFFFF +3 (turns) FF00FF +4 (α-helix) FF0000 +5 FFA500 -3 00FFFF -4 00FF00 other (β-sheet) FFFF00 base pairs FF8080
- JmolConstants.java
- Colors used by Rasmol and Chime (RasMol 2.6β2, Eric Martz, http://www.umass.edu/microbio/rasmol/).
- Colors used by Rasmol (official Rasmol 2.7.3 manual, http://openrasmol.org/).
- DRuMS color scheme (still to be fully incorporated here).
- Jmol-users and Jmol-developers mailing lists.
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
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 #0000CC #0033CC #0066CC #0099CC #00CCCC #00FFCC #0000FF #0033FF #0066FF #0099FF #00CCFF #00FFFF #330000 #333300 #336600 #339900 #33CC00 #33FF00 #330033 #333333 #336633 #339933 #33CC33 #33FF33 #330066 #333366 #336666 #339966 #33CC66 #33FF66 #330099 #333399 #336699 #339999 #33CC99 #33FF99 #3300CC #3333CC #3366CC #3399CC #33CCCC #33FFCC #3300FF #3333FF #3366FF #3399FF #33CCFF #33FFFF #660000 #663300 #666600 #669900 #66CC00 #66FF00 #660033 #663333 #666633 #669933 #66CC33 #66FF33 #660066 #663366 #666666 #669966 #66CC66 #66FF66 #660099 #663399 #666699 #669999 #66CC99 #66FF99 #6600CC #6633CC #6666CC #6699CC #66CCCC #66FFCC #6600FF #6633FF #6666FF #6699FF #66CCFF #66FFFF #990000 #993300 #996600 #999900 #99CC00 #99FF00 #990033 #993333 #996633 #999933 #99CC33 #99FF33 #990066 #993366 #996666 #999966 #99CC66 #99FF66 #990099 #993399 #996699 #999999 #99CC99 #99FF99 #9900CC #9933CC #9966CC #9999CC #99CCCC #99FFCC #9900FF #9933FF #9966FF #9999FF #99CCFF #99FFFF #CC0000 #CC3300 #CC6600 #CC9900 #CCCC00 #CCFF00 #CC0033 #CC3333 #CC6633 #CC9933 #CCCC33 #CCFF33 #CC0066 #CC3366 #CC6666 #CC9966 #CCCC66 #CCFF66 #CC0099 #CC3399 #CC6699 #CC9999 #CCCC99 #CCFF99 #CC00CC #CC33CC #CC66CC #CC99CC #CCCCCC #CCFFCC #CC00FF #CC33FF #CC66FF #CC99FF #CCCCFF #CCFFFF #FF0000 #FF3300 #FF6600 #FF9900 #FFCC00 #FFFF00 #FF0033 #FF3333 #FF6633 #FF9933 #FFCC33 #FFFF33 #FF0066 #FF3366 #FF6666 #FF9966 #FFCC66 #FFFF66 #FF0099 #FF3399 #FF6699 #FF9999 #FFCC99 #FFFF99 #FF00CC #FF33CC #FF66CC #FF99CC #FFCCCC #FFFFCC #FF00FF #FF33FF #FF66FF #FF99FF #FFCCFF #FFFFFF