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)
#
def color_h(selection="(all)"):
        s = str(selection)
        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","(resn ile and "+s+")")
        cmd.color("color_phe","(resn phe and "+s+")")
        cmd.color("color_val","(resn val and "+s+")")
        cmd.color("color_leu","(resn leu and "+s+")")
        cmd.color("color_trp","(resn trp and "+s+")")
        cmd.color("color_met","(resn met and "+s+")")
        cmd.color("color_ala","(resn ala and "+s+")")
        cmd.color("color_gly","(resn gly and "+s+")")
        cmd.color("color_cys","(resn cys and "+s+")")
        cmd.color("color_tyr","(resn tyr and "+s+")")
        cmd.color("color_pro","(resn pro and "+s+")")
        cmd.color("color_thr","(resn thr and "+s+")")
        cmd.color("color_ser","(resn ser and "+s+")")
        cmd.color("color_his","(resn his and "+s+")")
        cmd.color("color_glu","(resn glu and "+s+")")
        cmd.color("color_asn","(resn asn and "+s+")")
        cmd.color("color_gln","(resn gln and "+s+")")
        cmd.color("color_asp","(resn asp and "+s+")")
        cmd.color("color_lys","(resn lys and "+s+")")
        cmd.color("color_arg","(resn arg and "+s+")")
cmd.extend('color_h',color_h)

def color_h2(selection="(all)"):
	cmd.set_color("color_ile",[0.938,1,0.938])
	cmd.set_color("color_phe",[0.891,1,0.891])
	cmd.set_color("color_val",[0.844,1,0.844])
	cmd.set_color("color_leu",[0.793,1,0.793])
	cmd.set_color("color_trp",[0.746,1,0.746])
	cmd.set_color("color_met",[0.699,1,0.699])
	cmd.set_color("color_ala",[0.652,1,0.652])
	cmd.set_color("color_gly",[0.606,1,0.606])
	cmd.set_color("color_cys",[0.555,1,0.555])
	cmd.set_color("color_tyr",[0.508,1,0.508])
	cmd.set_color("color_pro",[0.461,1,0.461])
	cmd.set_color("color_thr",[0.414,1,0.414])
	cmd.set_color("color_ser",[0.363,1,0.363])
	cmd.set_color("color_his",[0.316,1,0.316])
	cmd.set_color("color_glu",[0.27,1,0.27])
	cmd.set_color("color_asn",[0.223,1,0.223])
	cmd.set_color("color_gln",[0.176,1,0.176])
	cmd.set_color("color_asp",[0.125,1,0.125])
	cmd.set_color("color_lys",[0.078,1,0.078])
	cmd.set_color("color_arg",[0.031,1,0.031])
	cmd.color("color_ile","(resn ile)")
	cmd.color("color_phe","(resn phe)")
	cmd.color("color_val","(resn val)")
	cmd.color("color_leu","(resn leu)")
	cmd.color("color_trp","(resn trp)")
	cmd.color("color_met","(resn met)")
	cmd.color("color_ala","(resn ala)")
	cmd.color("color_gly","(resn gly)")
	cmd.color("color_cys","(resn cys)")
	cmd.color("color_tyr","(resn tyr)")
	cmd.color("color_pro","(resn pro)")
	cmd.color("color_thr","(resn thr)")
	cmd.color("color_ser","(resn ser)")
	cmd.color("color_his","(resn his)")
	cmd.color("color_glu","(resn glu)")
	cmd.color("color_asn","(resn asn)")
	cmd.color("color_gln","(resn gln)")
	cmd.color("color_asp","(resn asp)")
	cmd.color("color_lys","(resn lys)")
	cmd.color("color_arg","(resn arg)")
cmd.extend('color_h2',color_h2)