Spectrum

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Spectrum ex2.png

Overview

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

Usage

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

expression

count, b, q, or pc: respectively, atom count, temperature factor, occupancy, or partial charge {default: count}

palette

string: palette name {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

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