Color h

Overview

This script colors the selection passed in based on the hydrophobicity scale as defined by:

Source: http://us.expasy.org/tools/pscale/Hphob.Eisenberg.html

Amino acid scale: Normalized consensus hydrophobicity scale

Author(s): Eisenberg D., Schwarz E., Komarony M., Wall R.

Reference: J. Mol. Biol. 179:125-142 (1984)

Or check out hydrophobicity coloring, with rTools from Kristian Rother. http://www.rubor.de/pymol_extensions_de.html

The Code

# color_h
# -------
 
# PyMOL command to color protein molecules according to the Eisenberg hydrophobicity scale
 
#
# Source: http://us.expasy.org/tools/pscale/Hphob.Eisenberg.html
# Amino acid scale: Normalized consensus hydrophobicity scale
# Author(s): Eisenberg D., Schwarz E., Komarony M., Wall R.
# Reference: J. Mol. Biol. 179:125-142 (1984)
#
# Amino acid scale values:
#
# Ala:  0.620
# Arg: -2.530
# Asn: -0.780
# Asp: -0.900
# Cys:  0.290
# Gln: -0.850
# Glu: -0.740
# Gly:  0.480
# His: -0.400
# Ile:  1.380
# Leu:  1.060
# Lys: -1.500
# Met:  0.640
# Phe:  1.190
# Pro:  0.120
# Ser: -0.180
# Thr: -0.050
# Trp:  0.810
# Tyr:  0.260
# Val:  1.080
#
# Usage:
# color_h (selection)
#
from pymol import cmd

def color_h(selection='all'):
        s = str(selection)
	print s
        cmd.set_color('color_ile',[0.996,0.062,0.062])
        cmd.set_color('color_phe',[0.996,0.109,0.109])
        cmd.set_color('color_val',[0.992,0.156,0.156])
        cmd.set_color('color_leu',[0.992,0.207,0.207])
        cmd.set_color('color_trp',[0.992,0.254,0.254])
        cmd.set_color('color_met',[0.988,0.301,0.301])
        cmd.set_color('color_ala',[0.988,0.348,0.348])
        cmd.set_color('color_gly',[0.984,0.394,0.394])
        cmd.set_color('color_cys',[0.984,0.445,0.445])
        cmd.set_color('color_tyr',[0.984,0.492,0.492])
        cmd.set_color('color_pro',[0.980,0.539,0.539])
        cmd.set_color('color_thr',[0.980,0.586,0.586])
        cmd.set_color('color_ser',[0.980,0.637,0.637])
        cmd.set_color('color_his',[0.977,0.684,0.684])
        cmd.set_color('color_glu',[0.977,0.730,0.730])
        cmd.set_color('color_asn',[0.973,0.777,0.777])
        cmd.set_color('color_gln',[0.973,0.824,0.824])
        cmd.set_color('color_asp',[0.973,0.875,0.875])
        cmd.set_color('color_lys',[0.899,0.922,0.922])
        cmd.set_color('color_arg',[0.899,0.969,0.969])
        cmd.color("color_ile","("+s+" and resn ile)")
        cmd.color("color_phe","("+s+" and resn phe)")
        cmd.color("color_val","("+s+" and resn val)")
        cmd.color("color_leu","("+s+" and resn leu)")
        cmd.color("color_trp","("+s+" and resn trp)")
        cmd.color("color_met","("+s+" and resn met)")
        cmd.color("color_ala","("+s+" and resn ala)")
        cmd.color("color_gly","("+s+" and resn gly)")
        cmd.color("color_cys","("+s+" and resn cys)")
        cmd.color("color_tyr","("+s+" and resn tyr)")
        cmd.color("color_pro","("+s+" and resn pro)")
        cmd.color("color_thr","("+s+" and resn thr)")
        cmd.color("color_ser","("+s+" and resn ser)")
        cmd.color("color_his","("+s+" and resn his)")
        cmd.color("color_glu","("+s+" and resn glu)")
        cmd.color("color_asn","("+s+" and resn asn)")
        cmd.color("color_gln","("+s+" and resn gln)")
        cmd.color("color_asp","("+s+" and resn asp)")
        cmd.color("color_lys","("+s+" and resn lys)")
        cmd.color("color_arg","("+s+" and resn arg)")
cmd.extend('color_h',color_h)

def color_h2(selection='all'):
        s = str(selection)
	print s
	cmd.set_color("color_ile2",[0.938,1,0.938])
	cmd.set_color("color_phe2",[0.891,1,0.891])
	cmd.set_color("color_val2",[0.844,1,0.844])
	cmd.set_color("color_leu2",[0.793,1,0.793])
	cmd.set_color("color_trp2",[0.746,1,0.746])
	cmd.set_color("color_met2",[0.699,1,0.699])
	cmd.set_color("color_ala2",[0.652,1,0.652])
	cmd.set_color("color_gly2",[0.606,1,0.606])
	cmd.set_color("color_cys2",[0.555,1,0.555])
	cmd.set_color("color_tyr2",[0.508,1,0.508])
	cmd.set_color("color_pro2",[0.461,1,0.461])
	cmd.set_color("color_thr2",[0.414,1,0.414])
	cmd.set_color("color_ser2",[0.363,1,0.363])
	cmd.set_color("color_his2",[0.316,1,0.316])
	cmd.set_color("color_glu2",[0.27,1,0.27])
	cmd.set_color("color_asn2",[0.223,1,0.223])
	cmd.set_color("color_gln2",[0.176,1,0.176])
	cmd.set_color("color_asp2",[0.125,1,0.125])
	cmd.set_color("color_lys2",[0.078,1,0.078])
	cmd.set_color("color_arg2",[0.031,1,0.031])
        cmd.color("color_ile2","("+s+" and resn ile)")
        cmd.color("color_phe2","("+s+" and resn phe)")
        cmd.color("color_val2","("+s+" and resn val)")
        cmd.color("color_leu2","("+s+" and resn leu)")
        cmd.color("color_trp2","("+s+" and resn trp)")
        cmd.color("color_met2","("+s+" and resn met)")
        cmd.color("color_ala2","("+s+" and resn ala)")
        cmd.color("color_gly2","("+s+" and resn gly)")
        cmd.color("color_cys2","("+s+" and resn cys)")
        cmd.color("color_tyr2","("+s+" and resn tyr)")
        cmd.color("color_pro2","("+s+" and resn pro)")
        cmd.color("color_thr2","("+s+" and resn thr)")
        cmd.color("color_ser2","("+s+" and resn ser)")
        cmd.color("color_his2","("+s+" and resn his)")
        cmd.color("color_glu2","("+s+" and resn glu)")
        cmd.color("color_asn2","("+s+" and resn asn)")
        cmd.color("color_gln2","("+s+" and resn gln)")
        cmd.color("color_asp2","("+s+" and resn asp)")
        cmd.color("color_lys2","("+s+" and resn lys)")
        cmd.color("color_arg2","("+s+" and resn arg)")
cmd.extend('color_h2',color_h2)