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

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

# 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

Spectrum

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