How can I evaluate the hydrophobicity of a protein with PyMol?

Open Pymol and load up your protein of choice. Download color_h.py which is a script from the University of Osaka that colours the residues according to Eisenberg's scale of hydrophobicity. Load this into Pymol by File->Run->PATH/TO/color_h.py. Then in Pymol run the following commands:

show surface
color_h

# 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)
# https://protein-sol.manchester.ac.uk/ 
# https://www.nature.com/articles/s41598-018-36950-8 
# Amino acid scale values:
#
# Ile:	1.38	[0.996,0.062,0.062]
# Phe:	1.19	[0.996,0.109,0.109]
# Val:	1.08	[0.992,0.156,0.156]
# Leu:	1.06	[0.992,0.207,0.207]
# Trp:	0.81	[0.992,0.254,0.254]
# Met:	0.64	[0.988,0.301,0.301]
# Ala:	0.62	[0.988,0.348,0.348]
# Gly:	0.48	[0.984,0.394,0.394]
# Cys:	0.29	[0.984,0.445,0.445]
# Tyr:	0.26	[0.984,0.492,0.492]
# Pro:	0.12	[0.980,0.539,0.539]
# Thr:	-0.05	[0.980,0.586,0.586]
# Ser:	-0.18	[0.980,0.637,0.637]
# His:	-0.4	[0.977,0.684,0.684]
# Glu:	-0.74	[0.977,0.730,0.730]
# Asn:	-0.78	[0.973,0.777,0.777]
# Gln:	-0.85	[0.973,0.824,0.824]
# Asp:	-0.9	[0.973,0.875,0.875]
# Lys:	-1.5	[0.899,0.922,0.922]
# Arg:	-2.53	[0.899,0.969,0.969]
#
# load https://shaker.umh.es/computing/hydrophobic.pdb
# extract ligand, organic
# show surface
# File->Run->PATH/TO/color_h.py
# color_h
# ramp_new prox, ligand, [1.38, 1.19, 1.08, 1.06, 0.81, 0.64, 0.62, 0.48, 0.29, 0.26, 0.12, -0.05, -0.18, -0.4, -0.74, -0.78, -0.85, -0.9, -1.5, -2.53], [[0.996,0.062,0.062], [0.996,0.109,0.109], [0.992,0.156,0.156], [0.992,0.207,0.207], [0.992,0.254,0.254], [0.988,0.301,0.301], [0.988,0.348,0.348], [0.984,0.394,0.394], [0.984,0.445,0.445], [0.984,0.492,0.492], [0.980,0.539,0.539], [0.980,0.586,0.586], [0.980,0.637,0.637], [0.977,0.684,0.684], [0.977,0.730,0.730], [0.973,0.777,0.777], [0.973,0.824,0.824], [0.973,0.875,0.875], [0.899,0.922,0.922], [0.899,0.969,0.969]]
#
# 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)



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