Color Values: Difference between revisions

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**American and English spellings of gray/grey and color/colour can be used
**American and English spellings of gray/grey and color/colour can be used
*Sources
*Sources
**Pymol colours are specified as triples of independent Red, Green and Blue contribution in range 0-1.0
**Pymol colours are specified as triples of independent Red, Green and Blue contribution in range 0-1.0 in square brackets (e.g. [1.0,1.0,1.0] for white)
**Colour specs from source files Color.c, menu.py and appearance.py of Pymol 0.99 beta29
**Colour specs from source files Color.c, menu.py and appearance.py of Pymol 0.99 beta29
**Colour names can be defined/redefined using set_color command or interactively in Colors item within Setting menu
**Colour names can be defined/redefined using set_color command or interactively in Colors item within Setting menu
Line 19: Line 19:
==Color by Element/Atom==
==Color by Element/Atom==


[[Advanced_Coloring#Coloring_by_atom_type]]
[[Advanced_Coloring#Coloring_by_atom_type | See: Color by Atom]]


==Simple named colours==
==Simple named colours==
Line 226: Line 226:
|- align="center"
|- align="center"
|bgcolor="#a036d3"| ||californium||0.631372549||0.211764706||0.831372549||
|bgcolor="#a036d3"| ||californium||0.631372549||0.211764706||0.831372549||
|- align="center"
|bgcolor="#33ff33"| ||carbon||0.2||1.0||0.2||
|- align="center"
|- align="center"
|bgcolor="#ffffc7"| ||cerium||1.000000000||1.000000000||0.780392157||
|bgcolor="#ffffc7"| ||cerium||1.000000000||1.000000000||0.780392157||
Line 274: Line 276:
|- align="center"
|- align="center"
|bgcolor="#00ff9c"| ||holmium||0.000000000||1.000000000||0.611764706||
|bgcolor="#00ff9c"| ||holmium||0.000000000||1.000000000||0.611764706||
|- align="center"
|bgcolor="#e5e5e5"| ||hydrogen||0.9||0.9||0.9||
|- align="center"
|- align="center"
|bgcolor="#a57472"| ||indium||0.650980392||0.458823529||0.450980392||
|bgcolor="#a57472"| ||indium||0.650980392||0.458823529||0.450980392||
Line 316: Line 320:
|- align="center"
|- align="center"
|bgcolor="#72c2c8"| ||niobium||0.450980392||0.760784314||0.788235294||
|bgcolor="#72c2c8"| ||niobium||0.450980392||0.760784314||0.788235294||
|- align="center"
|bgcolor="#3333ff"| ||nitrogen||0.2||0.2||1.0||
|- align="center"
|- align="center"
|bgcolor="#bd0c87"| ||nobelium||0.741176471||0.050980392||0.529411765||
|bgcolor="#bd0c87"| ||nobelium||0.741176471||0.050980392||0.529411765||
|- align="center"
|- align="center"
|bgcolor="#266695"| ||osmium||0.149019608||0.400000000||0.588235294||
|bgcolor="#266695"| ||osmium||0.149019608||0.400000000||0.588235294||
|- align="center"
|bgcolor="#ff4c4c"| ||oxygen||1.0||0.3||0.3||
|- align="center"
|- align="center"
|bgcolor="#006984"| ||palladium||0.000000000||0.411764706||0.521568627||
|bgcolor="#006984"| ||palladium||0.000000000||0.411764706||0.521568627||
Line 368: Line 376:
|- align="center"
|- align="center"
|bgcolor="#00ff00"| ||strontium||0.000000000||1.000000000||0.000000000||
|bgcolor="#00ff00"| ||strontium||0.000000000||1.000000000||0.000000000||
|- align="center"
|bgcolor="#e5c53f"| ||sulfur||0.9||0.775||0.25||
|- align="center"
|- align="center"
|bgcolor="#4ca5ff"| ||tantalum||0.301960784||0.650980392||1.000000000||
|bgcolor="#4ca5ff"| ||tantalum||0.301960784||0.650980392||1.000000000||
Line 619: Line 629:
|- align="center"  
|- align="center"  
|bgcolor="#00ffff"|cyan||bgcolor="#ff00ff"|magenta||bgcolor="#ff9999"|salmon
|bgcolor="#00ffff"|cyan||bgcolor="#ff00ff"|magenta||bgcolor="#ff9999"|salmon
|- align="center"
|bgcolor="#00ffff"|cyan||bgcolor="#ff0000"|red||bgcolor="#ff00ff"|magenta
|}
|}
==Carbon colour schemes==
==Carbon colour schemes==
*Accessible from 'by element' section within Colour submenu of object
*Accessible from 'by element' section within Colour submenu of object

Latest revision as of 04:39, 2 August 2010

Background

  • Naming
    • All listed colours can be specified by name (eg color red, mymolecule)
    • American and English spellings of gray/grey and color/colour can be used
  • Sources
    • Pymol colours are specified as triples of independent Red, Green and Blue contribution in range 0-1.0 in square brackets (e.g. [1.0,1.0,1.0] for white)
    • Colour specs from source files Color.c, menu.py and appearance.py of Pymol 0.99 beta29
    • Colour names can be defined/redefined using set_color command or interactively in Colors item within Setting menu

Spectral range colours

Spectral ranges are available by name including numerical value (eg grey56, s532)

  • Grays from 'gray00' to 'gray99' (white to black)
  • Spectrum from 's000' to 's999' (violet to red)
  • Original spectrum with extra blue and red at ends from 'o000' to 'o999'
  • Reversed offset spectrum from 'r000' to 'r999'
  • Complementary spectrum from 'c000' to 'c999'
  • Complementary spectrum separated by white from 'w000' to 'w999'

See Colour.c in source code for details about how spectra are calculated

Color by Element/Atom

See: Color by Atom

Simple named colours

  name R G B note
  aquamarine 0.5 1.0 1.0
  black 0.0 0.0 0.0
  blue 0.0 0.0 1.0
  bluewhite 0.85 0.85 1.00
  br0 0.1 0.1 1.0
  br1 0.2 0.1 0.9
  br2 0.3 0.1 0.8
  br3 0.4 0.1 0.7
  br4 0.5 0.1 0.6
  br5 0.6 0.1 0.5
  br6 0.7 0.1 0.4
  br7 0.8 0.1 0.3
  br8 0.9 0.1 0.2
  br9 1.0 0.1 0.1
  brightorange 1.0 0.7 0.2
  brown 0.65 0.32 0.17
  carbon 0.2 1.0 0.2
  chartreuse 0.5 1.0 0.0
  chocolate 0.555 0.222 0.111
  cyan 0.0 1.0 1.0
  darksalmon 0.73 0.55 0.52
  dash 1.0 1.0 0.0
  deepblue 0.25 0.25 0.65 deep
  deepolive 0.6 0.6 0.1
  deeppurple 0.6 0.1 0.6
  deepsalmon 1.0 0.5 0.5 duplicated?
  deepsalmon 1.00 0.42 0.42 duplicated?
  deepteal 0.1 0.6 0.6
  density 0.1 0.1 0.6
  dirtyviolet 0.70 0.50 0.50
  firebrick 0.698 0.13 0.13
  forest 0.2 0.6 0.2
  gray 0.5 0.5 0.5 american spelling
  green 0.0 1.0 0.0
  greencyan 0.25 1.00 0.75
  grey 0.5 0.5 0.5 english spelling
  hotpink 1.0 0.0 0.5
  hydrogen 0.9 0.9 0.9
  lightblue 0.75 0.75 1.0
  lightmagenta 1.0 0.2 0.8
  lightorange 1.0 0.8 0.5
  lightpink 1.00 0.75 0.87
  lightteal 0.4 0.7 0.7
  lime 0.5 1.0 0.5
  limegreen 0.0 1.0 0.5
  limon 0.75 1.00 0.25
  magenta 1.0 0.0 1.0
  marine 0.0 0.5 1.0
  nitrogen 0.2 0.2 1.0
  olive 0.77 0.70 0.00
  orange 1.0 0.5 0.0
  oxygen 1.0 0.3 0.3
  palecyan 0.8 1.0 1.0
  palegreen 0.65 0.9 0.65
  paleyellow 1.0 1.0 0.5
  pink 1.0 0.65 0.85
  purple 0.75 0.00 0.75
  purpleblue 0.5 0.0 1.0 legacy name
  raspberry 0.70 0.30 0.40
  red 1.0 0.0 0.0
  ruby 0.6 0.2 0.2
  salmon 1.0 0.6 0.6 was 0.5
  sand 0.72 0.55 0.30
  skyblue 0.20 0.50 0.80
  slate 0.5 0.5 1.0
  smudge 0.55 0.70 0.40
  splitpea 0.52 0.75 0.00
  sulfur 0.9 0.775 0.25 far enough from yellow
  teal 0.00 0.75 0.75
  tv_blue 0.3 0.3 1.0
  tv_green 0.2 1.0 0.2
  tv_orange 1.0 0.55 0.15
  tv_red 1.0 0.2 0.2
  tv_yellow 1.0 1.0 0.2
  violet 1.0 0.5 1.0
  violetpurple 0.55 0.25 0.60
  warmpink 0.85 0.20 0.50
  wheat 0.99 0.82 0.65
  white 1.0 1.0 1.0
  yellow 1.0 1.0 0.0
  yelloworange 1.0 0.87 0.37

Chemical element colours

  name R G B note
  actinium 0.439215686 0.670588235 0.980392157
  aluminum 0.749019608 0.650980392 0.650980392
  americium 0.329411765 0.360784314 0.949019608
  antimony 0.619607843 0.388235294 0.709803922
  argon 0.501960784 0.819607843 0.890196078
  arsenic 0.741176471 0.501960784 0.890196078
  astatine 0.458823529 0.309803922 0.270588235
  barium 0.000000000 0.788235294 0.000000000
  berkelium 0.541176471 0.309803922 0.890196078
  beryllium 0.760784314 1.000000000 0.000000000
  bismuth 0.619607843 0.309803922 0.709803922
  bohrium 0.878431373 0.000000000 0.219607843
  boron 1.000000000 0.709803922 0.709803922
  bromine 0.650980392 0.160784314 0.160784314
  cadmium 1.000000000 0.850980392 0.560784314
  calcium 0.239215686 1.000000000 0.000000000
  californium 0.631372549 0.211764706 0.831372549
  carbon 0.2 1.0 0.2
  cerium 1.000000000 1.000000000 0.780392157
  cesium 0.341176471 0.090196078 0.560784314
  chlorine 0.121568627 0.941176471 0.121568627
  chromium 0.541176471 0.600000000 0.780392157
  cobalt 0.941176471 0.564705882 0.627450980
  copper 0.784313725 0.501960784 0.200000000
  curium 0.470588235 0.360784314 0.890196078
  deuterium 0.9 0.9 0.9
  dubnium 0.819607843 0.000000000 0.309803922
  dysprosium 0.121568627 1.000000000 0.780392157
  einsteinium 0.701960784 0.121568627 0.831372549
  erbium 0.000000000 0.901960784 0.458823529
  europium 0.380392157 1.000000000 0.780392157
  fermium 0.701960784 0.121568627 0.729411765
  fluorine 0.701960784 1.000000000 1.000000000
  francium 0.258823529 0.000000000 0.400000000
  gadolinium 0.270588235 1.000000000 0.780392157
  gallium 0.760784314 0.560784314 0.560784314
  germanium 0.400000000 0.560784314 0.560784314
  gold 1.000000000 0.819607843 0.137254902
  hafnium 0.301960784 0.760784314 1.000000000
  hassium 0.901960784 0.000000000 0.180392157
  helium 0.850980392 1.000000000 1.000000000
  holmium 0.000000000 1.000000000 0.611764706
  hydrogen 0.9 0.9 0.9
  indium 0.650980392 0.458823529 0.450980392
  iodine 0.580392157 0.000000000 0.580392157
  iridium 0.090196078 0.329411765 0.529411765
  iron 0.878431373 0.400000000 0.200000000
  krypton 0.360784314 0.721568627 0.819607843
  lanthanum 0.439215686 0.831372549 1.000000000
  lawrencium 0.780392157 0.000000000 0.400000000
  lead 0.341176471 0.349019608 0.380392157
  lithium 0.800000000 0.501960784 1.000000000
  lutetium 0.000000000 0.670588235 0.141176471
  magnesium 0.541176471 1.000000000 0.000000000
  manganese 0.611764706 0.478431373 0.780392157
  meitnerium 0.921568627 0.000000000 0.149019608
  mendelevium 0.701960784 0.050980392 0.650980392
  mercury 0.721568627 0.721568627 0.815686275
  molybdenum 0.329411765 0.709803922 0.709803922
  neodymium 0.780392157 1.000000000 0.780392157
  neon 0.701960784 0.890196078 0.960784314
  neptunium 0.000000000 0.501960784 1.000000000
  nickel 0.313725490 0.815686275 0.313725490
  niobium 0.450980392 0.760784314 0.788235294
  nitrogen 0.2 0.2 1.0
  nobelium 0.741176471 0.050980392 0.529411765
  osmium 0.149019608 0.400000000 0.588235294
  oxygen 1.0 0.3 0.3
  palladium 0.000000000 0.411764706 0.521568627
  phosphorus 1.000000000 0.501960784 0.000000000
  platinum 0.815686275 0.815686275 0.878431373
  plutonium 0.000000000 0.419607843 1.000000000
  polonium 0.670588235 0.360784314 0.000000000
  potassium 0.560784314 0.250980392 0.831372549
  praseodymium 0.850980392 1.000000000 0.780392157
  promethium 0.639215686 1.000000000 0.780392157
  protactinium 0.000000000 0.631372549 1.000000000
  radium 0.000000000 0.490196078 0.000000000
  radon 0.258823529 0.509803922 0.588235294
  rhenium 0.149019608 0.490196078 0.670588235
  rhodium 0.039215686 0.490196078 0.549019608
  rubidium 0.439215686 0.180392157 0.690196078
  ruthenium 0.141176471 0.560784314 0.560784314
  rutherfordium 0.800000000 0.000000000 0.349019608
  samarium 0.560784314 1.000000000 0.780392157
  scandium 0.901960784 0.901960784 0.901960784
  seaborgium 0.850980392 0.000000000 0.270588235
  selenium 1.000000000 0.631372549 0.000000000
  silicon 0.941176471 0.784313725 0.627450980
  silver 0.752941176 0.752941176 0.752941176
  sodium 0.670588235 0.360784314 0.949019608
  strontium 0.000000000 1.000000000 0.000000000
  sulfur 0.9 0.775 0.25
  tantalum 0.301960784 0.650980392 1.000000000
  technetium 0.231372549 0.619607843 0.619607843
  tellurium 0.831372549 0.478431373 0.000000000
  terbium 0.188235294 1.000000000 0.780392157
  thallium 0.650980392 0.329411765 0.301960784
  thorium 0.000000000 0.729411765 1.000000000
  thulium 0.000000000 0.831372549 0.321568627
  tin 0.400000000 0.501960784 0.501960784
  titanium 0.749019608 0.760784314 0.780392157
  tungsten 0.129411765 0.580392157 0.839215686
  uranium 0.000000000 0.560784314 1.000000000
  vanadium 0.650980392 0.650980392 0.670588235
  xenon 0.258823529 0.619607843 0.690196078
  ytterbium 0.000000000 0.749019608 0.219607843
  yttrium 0.580392157 1.000000000 1.000000000
  zinc 0.490196078 0.501960784 0.690196078
  zirconium 0.580392157 0.878431373 0.878431373

Interactive menu colours

Accessible from Colour submenu of objects

reds

  name R G B
  red 1.0 0.0 0.0
  tv_red 1.0 0.2 0.2
  raspberry 0.70 0.30 0.40
  darksalmon 0.73 0.55 0.52
  salmon 1.0 0.6 0.6
  deepsalmon 1.00 0.42 0.42
  warmpink 0.85 0.20 0.50
  firebrick 0.698 0.13 0.13
  ruby 0.6 0.2 0.2
  chocolate 0.555 0.222 0.111
  brown 0.65 0.32 0.17

greens

  name R G B
  green 0.0 1.0 0.0
  tv_green 0.2 1.0 0.2
  chartreuse 0.5 1.0 0.0
  splitpea 0.52 0.75 0.00
  smudge 0.55 0.70 0.40
  palegreen 0.65 0.9 0.65
  limegreen 0.0 1.0 0.5
  lime 0.5 1.0 0.5
  limon 0.75 1.00 0.25
  forest 0.2 0.6 0.2

blues

  name R G B
  blue 0.0 0.0 1.0
  tv_blue 0.3 0.3 1.0
  marine 0.0 0.5 1.0
  slate 0.5 0.5 1.0
  lightblue 0.75 0.75 1.0
  skyblue 0.20 0.50 0.80
  purpleblue 0.5 0.0 1.0
  deepblue 0.25 0.25 0.65
  density 0.1 0.1 0.6

yellows

  name R G B
  yellow 1.0 1.0 0.0
  tv_yellow 1.0 1.0 0.2
  paleyellow 1.0 1.0 0.5
  yelloworange 1.0 0.87 0.37
  limon 0.75 1.00 0.25
  wheat 0.99 0.82 0.65
  sand 0.72 0.55 0.30

magentas

  name R G B
  magenta 1.0 0.0 1.0
  lightmagenta 1.0 0.2 0.8
  hotpink 1.0 0.0 0.5
  pink 1.0 0.65 0.85
  lightpink 1.00 0.75 0.87
  dirtyviolet 0.70 0.50 0.50
  violet 1.0 0.5 1.0
  violetpurple 0.55 0.25 0.60
  purple 0.75 0.00 0.75
  deeppurple 0.6 0.1 0.6

cyans

  name R G B
  cyan 0.0 1.0 1.0
  palecyan 0.8 1.0 1.0
  aquamarine 0.5 1.0 1.0
  greencyan 0.25 1.00 0.75
  teal 0.00 0.75 0.75
  deepteal 0.1 0.6 0.6
  lightteal 0.4 0.7 0.7

oranges

  name R G B
  orange 1.0 0.5 0.0
  tv_orange 1.0 0.55 0.15
  brightorange 1.0 0.7 0.2
  lightorange 1.0 0.8 0.5
  yelloworange 1.0 0.87 0.37
  olive 0.77 0.70 0.00
  deepolive 0.6 0.6 0.1

tints

  name R G B
  wheat 0.99 0.82 0.65
  palegreen 0.65 0.9 0.65
  lightblue 0.75 0.75 1.0
  paleyellow 1.0 1.0 0.5
  lightpink 1.00 0.75 0.87
  palecyan 0.8 1.0 1.0
  lightorange 1.0 0.8 0.5
  bluewhite 0.85 0.85 1.00

grays

  name R G B
  white 1.0 1.0 1.0
  grey90 0.9 0.9 0.9
  grey80 0.8 0.8 0.8
  grey70 0.7 0.7 0.7
  grey60 0.6 0.6 0.6
  grey50 0.5 0.5 0.5
  grey40 0.4 0.4 0.4
  grey30 0.3 0.3 0.3
  grey20 0.2 0.2 0.2
  grey10 0.1 0.1 0.1
  black 0.0 0.0 0.0

Secondary structure colour schemes

Accessible from 'by ss' section within Colour submenu of object

helix sheet loop
red yellow green
cyan magenta salmon
cyan red magenta

Carbon colour schemes

  • Accessible from 'by element' section within Colour submenu of object
  • Only carbon colour is affected, other elements are set to their default element colour
  • Separated into five sets:
    • main set
  name
  (carbon not changed)
  carbon
  cyan
  lightmagenta
  yellow
  salmon
  hydrogen
  slate
  orange
    • set2
  name
  lime
  deepteal
  hotpink
  yelloworange
  violetpurple
  grey70
  marine
  olive
    • set3
  name
  smudge
  teal
  dirtyviolet
  wheat
  deepsalmon
  lightpink
  aquamarine
  paleyellow
    • set4
  name
  limegreen
  skyblue
  warmpink
  limon
  violet
  bluewhite
  greencyan
  sand
    • set 5
  name
  forest
  lightteal
  darksalmon
  splitpea
  raspberry
  grey50
  deepblue
  brown
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