Color Expression
RGB values
A color can be specified by a comma separated triple of Red, Green and Blue (RGB) components enclosed in square brackets, where RGB values are from 0 to 255, respectively.
Predefined Color
The following 24 colors can be specified by their name.
| color name | RGB values | color |
| BLACK | [0, 0, 0] | |
| BLUE | [0, 0, 255] | |
| BLUETINT | [175, 214, 255] | |
| BROWN | [175, 117, 89] | |
| CYAN | [0, 255, 255] | |
| GOLD | [255, 156, 0] | |
| GREY | [125, 125, 125] | |
| GREEN | [0, 255, 0] | |
| GREENBLUE | [46, 139, 87] | |
| GreenTint | [152, 255, 179] | |
| HOTPINK | [255, 0, 101] | |
| MAGENTA | [255, 0, 255] | |
| ORANGE | [255, 165, 0] | |
| PINK | [255, 101, 117] | |
| PINKTINT | [255, 171, 187] | |
| PURPLE | [160, 32, 240] | |
| RED | [255, 0, 0] | |
| REDORANGE | [255, 69, 0] | |
| SEAGREEN | [0, 250, 109] | |
| SKYBLUE | [58, 144, 255] | |
| VIOLET | [238, 130, 238] | |
| WHITE | [255, 255, 255] | |
| YELLOW | [255, 255, 0] | |
| YELLOWTINT | [246, 246, 117] |
Color Scheme
amino
The color scheme 'amino' colors amino acids as follows.
| amino acids | RGB values | color |
| ASP, GLU | [230, 10, 10] | |
| CYS, MET | [230,230, 0] | |
| LYS, ARG | [20, 90,255] | |
| SER, THR | [250,150, 0] | |
| PHE, TYR | [50, 50,170] | |
| ASN, GLN | [0,220,220] | |
| GLY | [235,235,235] | |
| LEU, VAL, ILE | [15,130, 15] | |
| ALA | [200,200,200] | |
| TRP | [180, 90,180] | |
| HIS | [130,130,210] | |
| PRO | [220,150,130] | |
| Others | [190,160,110] |
chain
The color scheme 'chain' assigns each macromolecular chain a unique colour.
charge
The color scheme 'charge' colors atoms according to their temperature factor. High values are coloured in blue and lower values coloured in red.
cpk
The color scheme 'cpk' colors atoms according to the element type as follows.
| element | RGB values | color |
| C | [200, 200, 200] | |
| N | [143, 143, 255] | |
| O | [240, 0, 0] | |
| S | [255, 200, 50] | |
| H | [255, 255, 255] | |
| He | [255, 192, 203] | |
| F, Si, Au | [218, 165, 32] | |
| Na | [0, 0, 255] | |
| P, Fe, Ba | [255, 165, 0] | |
| Al, Ca, Ti, Cr, Mn, Ag | [128, 128, 144] | |
| Ni, Cu, Zn, Br | [165, 42, 42] | |
| I | [160, 32, 240] | |
| B, Cl | [0, 255, 0] | |
| Li | [178, 34, 34] | |
| Mg | [34, 139, 34] | |
| Others | [255, 20, 147] |
group
The color scheme 'group' colors residues by their position in a macromolecular chain. Each chain is drawn as a smooth spectrum from blue to red. The N terminus of proteins and 5' terminus of nucleic acids are colored red and the C terminus of proteins and 3' terminus of nucleic acids are drawn in blue.
shapely
The color scheme 'shapely' colors residues as follows.
| residue | RGB values | color |
| ALA | [140, 255, 140] | |
| GLY | [255, 255, 255] | |
| LEU | [69, 94, 69] | |
| SER | [255, 112, 66] | |
| VAL | [255, 140, 255] | |
| THR | [184, 76, 0] | |
| LYS | [71, 71, 184] | |
| ASP | [160, 0, 66] | |
| ILE | [0, 76, 0] | |
| ASN | [255, 124, 112] | |
| GLU | [102, 0, 0] | |
| PRO | [82, 82, 82] | |
| ARG | [0, 0, 124] | |
| PHE | [83, 76, 66] | |
| GLN | [255, 76, 76] | |
| TYR | [140, 112, 76] | |
| HIS | [112, 112, 255] | |
| CYS | [255, 255, 112] | |
| MET | [184, 160, 66] | |
| TRP | [79, 70, 0] | |
| A | [160, 160, 255] | |
| C | [255, 140, 75] | |
| G | [255, 112, 112] | |
| T | [160, 255, 160] | |
| Others | [255, 0, 255] |
structure
The color scheme 'structure' colors residues according to the secondary structure as follows.
| secondary structure | RGB values | color |
| alpha helix | [255, 0, 128] | |
| beta sheet | [255, 200, 0] | |
| turn | [96, 128, 255] | |
| none | [255, 255, 255] |
temperature
The color scheme 'temperature' colors atoms according to their temperature factor. High values are coloured in red and lower values coloured in blue.
type
This color scheme 'type' colors each hydrogen bond according to the distance along a protein chain between hydrogen bond donor and acceptor as follows.
| offset | RGB values | color |
| +2 | [255, 255, 255] | |
| +3 | [255, 0, 255] | |
| +4 | [255, 0, 0] | |
| +5 | [255, 165, 0] | |
| -3 | [0, 255, 255] | |
| -4 | [0, 255, 0] | |
| Others | [255, 255, 0] |