Re: [PyMOL] colouring by hydrophobicity

[Luca J. <luc...@ma...>]

> I was wondering if there is a way to colour by a structure by 
> hydrophobicity.

Hi Carly,

This is a quick hack I wrote some time ago, but it kind of does the 
job... (of course I see much room for improvement!)

# 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)

Hope this helps,

Luca

--------------------------------------------------------
Luca Jovine, Ph.D.
Department of Molecular, Cell & Developmental Biology
Mount Sinai School of Medicine
Annenberg Building, Room 25-18
One Gustave L. Levy Place, New York, NY 10029-6574, USA
Voice: +1.212.241-8620  FAX: +1.509.356-2832
E-Mail: luc...@ma... - luc...@ms...
W3: http://www.mssm.edu/students/jovinl02
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