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@white-flying-snowball(Mitsuki Shibagaki)

color_hスクリプトをHSD, HSEに対応させる

Last updated at Posted at 2024-12-06

pymolの拡張機能（？）である"color_h"を使用すると、タンパク質分子の残基ごとの疎水性に応じた色分けができる。

コードは以下の通り。これをcolor_h.pyとして保存し、
pymol上の OPENで読み込んだ後color_hで実行できる。

# 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)
#
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)

しかし、デフォルトではヒスチジンは"HIS"表記にしか対応していない。

CHARMM-GUIのPDB readerを使用すると、ヒスチジンはδ位に水素が付加されるため、HSD表記となる。
このままでは、color_hがHSDにのみ反映されないという結果になってしまう。

そこで、color_hを以下のように書き換えることで、HIS, HSD, HIEいずれの表記にも同じ疎水性スコアを割り当てるようにする。
ファイル名をcolor_h_HISedit.pyとでもしておき、保存して同様に使用する。

HISに対する処理を、
HSD, HSE (CHARMM)
HID, HIE (AMBER)
にも同様に行うようにしている。

留意点

HSP（プロトン化された状態）に関しては保留。
他の残基に関しても、プロトン化状態の酸性残基などは考慮できていないと考えられるので注意が必要。

# 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   # HSD, HSE, HID, HIE was added
# 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)
#
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_hsd',[0.977,0.684,0.684])
        cmd.set_color('color_hse',[0.977,0.684,0.684])
        cmd.set_color('color_hid',[0.977,0.684,0.684])
        cmd.set_color('color_hie',[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_hsd","("+s+" and resn hsd)")
        cmd.color("color_hse","("+s+" and resn hse)")
        cmd.color("color_hid","("+s+" and resn hid)")
        cmd.color("color_hie","("+s+" and resn hie)")
        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_hsd2",[0.316,1,0.316])
        cmd.set_color("color_hse2",[0.316,1,0.316])
        cmd.set_color("color_hid2",[0.316,1,0.316])
        cmd.set_color("color_hie2",[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_hsd2","("+s+" and resn hsd)")
        cmd.color("color_hse2","("+s+" and resn hse)")
        cmd.color("color_hid2","("+s+" and resn hid)")
        cmd.color("color_hie2","("+s+" and resn hie)")
        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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