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128 lines
5.1 KiB
Python
128 lines
5.1 KiB
Python
# color_h
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# -------
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# PyMOL command to color protein molecules according to the Eisenberg hydrophobicity scale
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#
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# Source: http://us.expasy.org/tools/pscale/Hphob.Eisenberg.html
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# Amino acid scale: Normalized consensus hydrophobicity scale
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# Author(s): Eisenberg D., Schwarz E., Komarony M., Wall R.
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# Reference: J. Mol. Biol. 179:125-142 (1984)
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#
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# Amino acid scale values:
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#
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# Ala: 0.620
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# Arg: -2.530
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# Asn: -0.780
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# Asp: -0.900
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# Cys: 0.290
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# Gln: -0.850
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# Glu: -0.740
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# Gly: 0.480
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# His: -0.400
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# Ile: 1.380
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# Leu: 1.060
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# Lys: -1.500
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# Met: 0.640
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# Phe: 1.190
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# Pro: 0.120
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# Ser: -0.180
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# Thr: -0.050
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# Trp: 0.810
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# Tyr: 0.260
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# Val: 1.080
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#
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# Usage:
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# color_h (selection)
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#
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from pymol import cmd
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def color_h(selection='all'):
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s = str(selection)
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print s
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cmd.set_color('color_ile',[0.996,0.062,0.062])
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cmd.set_color('color_phe',[0.996,0.109,0.109])
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cmd.set_color('color_val',[0.992,0.156,0.156])
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cmd.set_color('color_leu',[0.992,0.207,0.207])
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cmd.set_color('color_trp',[0.992,0.254,0.254])
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cmd.set_color('color_met',[0.988,0.301,0.301])
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cmd.set_color('color_ala',[0.988,0.348,0.348])
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cmd.set_color('color_gly',[0.984,0.394,0.394])
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cmd.set_color('color_cys',[0.984,0.445,0.445])
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cmd.set_color('color_tyr',[0.984,0.492,0.492])
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cmd.set_color('color_pro',[0.980,0.539,0.539])
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cmd.set_color('color_thr',[0.980,0.586,0.586])
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cmd.set_color('color_ser',[0.980,0.637,0.637])
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cmd.set_color('color_his',[0.977,0.684,0.684])
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cmd.set_color('color_glu',[0.977,0.730,0.730])
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cmd.set_color('color_asn',[0.973,0.777,0.777])
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cmd.set_color('color_gln',[0.973,0.824,0.824])
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cmd.set_color('color_asp',[0.973,0.875,0.875])
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cmd.set_color('color_lys',[0.899,0.922,0.922])
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cmd.set_color('color_arg',[0.899,0.969,0.969])
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cmd.color("color_ile","("+s+" and resn ile)")
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cmd.color("color_phe","("+s+" and resn phe)")
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cmd.color("color_val","("+s+" and resn val)")
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cmd.color("color_leu","("+s+" and resn leu)")
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cmd.color("color_trp","("+s+" and resn trp)")
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cmd.color("color_met","("+s+" and resn met)")
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cmd.color("color_ala","("+s+" and resn ala)")
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cmd.color("color_gly","("+s+" and resn gly)")
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cmd.color("color_cys","("+s+" and resn cys)")
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cmd.color("color_tyr","("+s+" and resn tyr)")
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cmd.color("color_pro","("+s+" and resn pro)")
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cmd.color("color_thr","("+s+" and resn thr)")
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cmd.color("color_ser","("+s+" and resn ser)")
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cmd.color("color_his","("+s+" and resn his)")
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cmd.color("color_glu","("+s+" and resn glu)")
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cmd.color("color_asn","("+s+" and resn asn)")
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cmd.color("color_gln","("+s+" and resn gln)")
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cmd.color("color_asp","("+s+" and resn asp)")
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cmd.color("color_lys","("+s+" and resn lys)")
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cmd.color("color_arg","("+s+" and resn arg)")
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cmd.extend('color_h',color_h)
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def color_h2(selection='all'):
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s = str(selection)
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print s
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cmd.set_color("color_ile2",[0.938,1,0.938])
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cmd.set_color("color_phe2",[0.891,1,0.891])
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cmd.set_color("color_val2",[0.844,1,0.844])
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cmd.set_color("color_leu2",[0.793,1,0.793])
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cmd.set_color("color_trp2",[0.746,1,0.746])
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cmd.set_color("color_met2",[0.699,1,0.699])
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cmd.set_color("color_ala2",[0.652,1,0.652])
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cmd.set_color("color_gly2",[0.606,1,0.606])
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cmd.set_color("color_cys2",[0.555,1,0.555])
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cmd.set_color("color_tyr2",[0.508,1,0.508])
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cmd.set_color("color_pro2",[0.461,1,0.461])
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cmd.set_color("color_thr2",[0.414,1,0.414])
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cmd.set_color("color_ser2",[0.363,1,0.363])
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cmd.set_color("color_his2",[0.316,1,0.316])
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cmd.set_color("color_glu2",[0.27,1,0.27])
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cmd.set_color("color_asn2",[0.223,1,0.223])
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cmd.set_color("color_gln2",[0.176,1,0.176])
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cmd.set_color("color_asp2",[0.125,1,0.125])
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cmd.set_color("color_lys2",[0.078,1,0.078])
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cmd.set_color("color_arg2",[0.031,1,0.031])
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cmd.color("color_ile2","("+s+" and resn ile)")
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cmd.color("color_phe2","("+s+" and resn phe)")
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cmd.color("color_val2","("+s+" and resn val)")
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cmd.color("color_leu2","("+s+" and resn leu)")
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cmd.color("color_trp2","("+s+" and resn trp)")
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cmd.color("color_met2","("+s+" and resn met)")
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cmd.color("color_ala2","("+s+" and resn ala)")
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cmd.color("color_gly2","("+s+" and resn gly)")
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cmd.color("color_cys2","("+s+" and resn cys)")
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cmd.color("color_tyr2","("+s+" and resn tyr)")
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cmd.color("color_pro2","("+s+" and resn pro)")
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cmd.color("color_thr2","("+s+" and resn thr)")
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cmd.color("color_ser2","("+s+" and resn ser)")
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cmd.color("color_his2","("+s+" and resn his)")
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cmd.color("color_glu2","("+s+" and resn glu)")
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cmd.color("color_asn2","("+s+" and resn asn)")
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cmd.color("color_gln2","("+s+" and resn gln)")
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cmd.color("color_asp2","("+s+" and resn asp)")
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cmd.color("color_lys2","("+s+" and resn lys)")
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cmd.color("color_arg2","("+s+" and resn arg)")
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cmd.extend('color_h2',color_h2) |