Spectrum

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:

# 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

• Advanced Coloring
• chainbow
• spectrumany