Difference between revisions of "Spectrum"

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m (Adding link to new page "Palette Colorbars" that will have colorbars for the various palettes.)
(1.6 updates)
 
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[[Image:Spectrum_ex2.png|right|thumb|185px]]
 
[[Image:Spectrum_ex2.png|right|thumb|185px]]
= Overview =
 
 
[[Spectrum]] colors atoms with a spectrum of colors based on an atomic property.
 
[[Spectrum]] colors atoms with a spectrum of colors based on an atomic property.
 
      
 
      
 +
''New in PyMOL 1.6: Supports any [[iterate]] expression, like [[spectrumany]]''
 +
 +
''New in PyMOL 1.6: Supports space separated color list as palette, like [[spectrumany]]''
 +
 
= Usage =
 
= Usage =
 
<source lang="python">
 
<source lang="python">
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''expression''
 
''expression''
::count, b, q, or pc: respectively, atom count, temperature factor, occupancy, or partial charge {default: count}
+
::count (atom count), pc (partial charge), or any expression which is valid for [[iterate]]. Non-numerical values will be enumerated (e.g. chain) {default: count}
 
      
 
      
 
''palette''
 
''palette''
::string: palette name {default: rainbow}
+
::string: palette name, or space separated list of colors {default: rainbow}
 
   
 
   
 
''selection''
 
''selection''
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*rainbow_cycle
 
*rainbow_cycle
 
*rainbow_cycle_rev  
 
*rainbow_cycle_rev  
*rainbow_rev red_blue
+
*rainbow_rev  
*red_cyan red_green
+
*red_blue
 +
*red_cyan  
 +
*red_green
 
*red_white_blue
 
*red_white_blue
 
*red_white_cyan
 
*red_white_cyan
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spectrum count, rainbow_rev, chain A, byres=1
 
spectrum count, rainbow_rev, chain A, byres=1
 
</source>
 
</source>
 +
 +
Non-numerical property (Since PyMOL 1.6):
 +
 +
spectrum chain
 +
 +
Custom color list (Since PyMOL 1.6):
 +
 +
spectrum b, blue yellow cyan neon pink grey
  
 
== Intermediate ==
 
== Intermediate ==
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* [[Advanced_Coloring#Coloring_with_.27chainbows.27_from_a_script|chainbow]]
 
* [[Advanced_Coloring#Coloring_with_.27chainbows.27_from_a_script|chainbow]]
 
* [[spectrumany]]
 
* [[spectrumany]]
 +
* [[Ramp_New]]
 +
* [[spectrumbar]]

Latest revision as of 13:56, 22 October 2019

Spectrum ex2.png

Spectrum colors atoms with a spectrum of colors based on an atomic property.

New in PyMOL 1.6: Supports any iterate expression, like spectrumany

New in PyMOL 1.6: Supports space separated color list as palette, like spectrumany

Usage

spectrum [expression [, palette [, selection [, minimum [, maximum [, byres ]]]]]]

expression

count (atom count), pc (partial charge), or any expression which is valid for iterate. Non-numerical values will be enumerated (e.g. chain) {default: count}

palette

string: palette name, or space separated list of colors {default: rainbow}

selection

string: atoms to color {default: (all)}

minimum

float: {default: None (automatic)}

maximum

float: {default: None (automatic)}

byres

integer: controls whether coloring is applied per-residue {default: 0}

Notes

Minimum and maximum are determined automatically unless both arguments are provided and minimum < maximum.

Available palettes include:

  • blue_green
  • blue_magenta
  • blue_red
  • blue_white_green
  • blue_white_magenta
  • blue_white_red
  • blue_white_yellow
  • blue_yellow
  • cbmr
  • cyan_magenta
  • cyan_red
  • cyan_white_magenta
  • cyan_white_red
  • cyan_white_yellow
  • cyan_yellow
  • gcbmry
  • green_blue
  • green_magenta
  • green_red
  • green_white_blue
  • green_white_magenta
  • green_white_red
  • green_white_yellow
  • green_yellow
  • green_yellow_red
  • magenta_blue
  • magenta_cyan
  • magenta_green
  • magenta_white_blue
  • magenta_white_cyan
  • magenta_white_green
  • magenta_white_yellow
  • magenta_yellow
  • rainbow
  • rainbow2
  • rainbow2_rev
  • rainbow_cycle
  • rainbow_cycle_rev
  • rainbow_rev
  • red_blue
  • red_cyan
  • red_green
  • red_white_blue
  • red_white_cyan
  • red_white_green
  • red_white_yellow
  • red_yellow
  • red_yellow_green
  • rmbc
  • yellow_blue
  • yellow_cyan
  • yellow_cyan_white
  • yellow_green
  • yellow_magenta
  • yellow_red
  • yellow_white_blue
  • yellow_white_green
  • yellow_white_magenta
  • yellow_white_red
  • yrmbcg

Examples

Simple

spectrum b, blue_red, minimum=10, maximum=50

spectrum count, rainbow_rev, chain A, byres=1

Non-numerical property (Since PyMOL 1.6):

spectrum chain

Custom color list (Since PyMOL 1.6):

spectrum b, blue yellow cyan neon pink grey

Intermediate

The following script will create this image:

Spectrum example.png

# color atoms based on their distance from a point
# returns the length of the distance between atom A and atom B

diff_len = lambda x,y : math.sqrt((x[0]-y[0])*(x[0]-y[0]) + (x[1]-y[1])*(x[1]-y[1]) + (x[2]-y[2])*(x[2]-y[2]))

# fetch 1hug from the PDB

fetch 1hug, async=0

# show it as surface

as surface

# create the pseudoatom at the origin

pseudoatom pOrig, pos=(0,0,0), label=origin

# these are special PyMOL variables that will hold # the coordinates of 
# the atoms and the  pseudoatom

stored.origCoord = []
stored.distCoord = []

# copy the coordinates into those special variables 

iterate_state 1, pOrig, stored.origCoord.append((x,y,z))
iterate_state 1, 1hug, stored.distCoord.append((x,y,z))

# extend origCoord to be the same length as the other

stored.origCoord *= len(stored.distCoord)

# calculate the distances

newB = map(lambda x,y: diff_len(x,y), stored.distCoord, stored.origCoord)

# put them into the b-factor of the protein

alter 1hug, b=newB.pop(0)

# color by rainbow_rev or any other
# palette listed in "help spectrum"

spectrum b, rainbow_rev, 1hug

See Also