Color h - Revision history

Cchem: 1 revision

2019-10-14T18:49:23Z

1 revision

Speleo3: python3

2019-10-09T10:43:16Z

python3

Pyadmin: 4 revisions

2014-03-28T02:15:06Z

4 revisions

Tlinnet: /* The Code */

2011-02-04T11:57:42Z

The Code

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Tlinnet: /* Overview */

2011-02-04T10:46:54Z

Overview

Tlinnet: /* The Code */

2011-02-04T10:45:05Z

The Code

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= 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)

= The Code =

<source lang="python">
# 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)

</source>

[[Category:Script_Library]]
[[Category:Biochemical_Scripts]]

@@ Line 53: / Line 53: @@
 def color_h(selection='all'):
          s = str(selection)
-	print s
+        print(s)
          cmd.set_color('color_ile',[0.996,0.062,0.062])
          cmd.set_color('color_phe',[0.996,0.109,0.109])
@@ Line 98: / Line 98: @@
 def color_h2(selection='all'):
          s = str(selection)
-	print s
+        print(s)
-	cmd.set_color("color_ile2",[0.938,1,0.938])
+        cmd.set_color("color_ile2",[0.938,1,0.938])
-	cmd.set_color("color_phe2",[0.891,1,0.891])
+        cmd.set_color("color_phe2",[0.891,1,0.891])
-	cmd.set_color("color_val2",[0.844,1,0.844])
+        cmd.set_color("color_val2",[0.844,1,0.844])
-	cmd.set_color("color_leu2",[0.793,1,0.793])
+        cmd.set_color("color_leu2",[0.793,1,0.793])
-	cmd.set_color("color_trp2",[0.746,1,0.746])
+        cmd.set_color("color_trp2",[0.746,1,0.746])
-	cmd.set_color("color_met2",[0.699,1,0.699])
+        cmd.set_color("color_met2",[0.699,1,0.699])
-	cmd.set_color("color_ala2",[0.652,1,0.652])
+        cmd.set_color("color_ala2",[0.652,1,0.652])
-	cmd.set_color("color_gly2",[0.606,1,0.606])
+        cmd.set_color("color_gly2",[0.606,1,0.606])
-	cmd.set_color("color_cys2",[0.555,1,0.555])
+        cmd.set_color("color_cys2",[0.555,1,0.555])
-	cmd.set_color("color_tyr2",[0.508,1,0.508])
+        cmd.set_color("color_tyr2",[0.508,1,0.508])
-	cmd.set_color("color_pro2",[0.461,1,0.461])
+        cmd.set_color("color_pro2",[0.461,1,0.461])
-	cmd.set_color("color_thr2",[0.414,1,0.414])
+        cmd.set_color("color_thr2",[0.414,1,0.414])
-	cmd.set_color("color_ser2",[0.363,1,0.363])
+        cmd.set_color("color_ser2",[0.363,1,0.363])
-	cmd.set_color("color_his2",[0.316,1,0.316])
+        cmd.set_color("color_his2",[0.316,1,0.316])
-	cmd.set_color("color_glu2",[0.27,1,0.27])
+        cmd.set_color("color_glu2",[0.27,1,0.27])
-	cmd.set_color("color_asn2",[0.223,1,0.223])
+        cmd.set_color("color_asn2",[0.223,1,0.223])
-	cmd.set_color("color_gln2",[0.176,1,0.176])
+        cmd.set_color("color_gln2",[0.176,1,0.176])
-	cmd.set_color("color_asp2",[0.125,1,0.125])
+        cmd.set_color("color_asp2",[0.125,1,0.125])
-	cmd.set_color("color_lys2",[0.078,1,0.078])
+        cmd.set_color("color_lys2",[0.078,1,0.078])
-	cmd.set_color("color_arg2",[0.031,1,0.031])
+        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)")

← Older revision	Revision as of 18:49, 14 October 2019
(No difference)

← Older revision	Revision as of 02:15, 28 March 2014
(No difference)

@@ Line 5: / Line 5: @@
 :: Author(s): Eisenberg D., Schwarz E., Komarony M., Wall R.
 ::Reference: J. Mol. Biol. 179:125-142 (1984)
 = The Code =