用PyMOL展示配体和受体相互作用的原子和氢键

转载于 https://mp.weixin.qq.com/s/P62sjqhSTxmWVicrEAk-RQ

为了简化展示过程，我们设计了一个pml脚本 (脚本内有很详细的解释)，只需要修改脚本里面受体和配体的名字，然后在PyMOL的命令行界面输入PyMOL> run display.pml即可获得展示结果。当然这个脚本也可以使用程序generatePmlForHbond.py生成。

 ############################################################
###All one needs to do is replacing:                        ##
###  * Protein structure file: E:\docking\1hsg_prot.pdb     ##
###  * Protein name: 1hsg                                   ##
###  * Docking result file: E:\docking\indinavir.pdbqt      ##
###  * Docking result name (normally ligand name): indinavir##
 ############################################################
# The following 4 lines:
    # 1. load protein structure and rename it
    # 2. add hydrogen (`h_add` uses a primitive algorithm to add hydrogens onto a molecule.)
    # 3. hide protein display
    # 4. show cartoon display for protein
load E:\yunpan\docking\1hsg_prot.pdb, 1hsg
h_add 1hsg
hide everything, 1hsg
show cartoon, 1hsg
cmd.spectrum("count", selection="1hsg", byres=1)

# The following 6 lines:
    # 1. load ligand structure and rename it
    # 2. add hydrogen
    # 3. hide ligand display
    # 4. show ligand in sticks mode
    # 5. Set width of stick to 0.15
    # 6. Set atom color: C-white;N-blue;O-red
load E:\yunpan\docking\indinavir.pdbqt, indinavir
h_add indinavir
hide everything, indinavir
show sticks, indinavir
set stick_radius, 0.15
util.cbaw indinavir

# The following 1 line:
    # 1. Select metal ions
select metals, symbol mg+ca+fe+zn

# The following 2 lines:
    # 1. Set hydrogen donator
    # 2. Set hydrogen accrptor
    # `select` creates a named selection from an atom selection.
    # `select name, (selection)`
select h_donator,  (elem n,o and (neighbor hydro))
select h_acceptor, (elem o or (elem n and not (neighbor hydro)))

# The following 4 lines:
    # 1. Create link between ligand_h_acceptor and prot_h_donator  within given distance 3.2
    # 2. Create link between ligand_h_donator  and prot_h_acceptor within given distance 3.2
    #    Set filter 3.6 for ideal geometry and filter 3.2 for minimally acceptable geometry
    # 3. Set red color for ligand_h_acceptor and prot_h_donator
    # 4. Set blue color for ligand_h_donator  and prot_h_acceptor
    # `distance` creates a new distance object between two selections. It will display all distances within the cutoff. Distance is also used to make hydrogen bonds like `distance hbonds, all, all, 3.2, mode=2`.
    # distance [ name [, selection1 [, selection2 [, cutoff [, mode ]]]]]
distance LaccPdon, (indinavir and h_acceptor), (1hsg and h_donator), 3.2
distance LdonPacc, (indinavir and h_donator), (1hsg and h_acceptor), 3.2
color red, LaccPdon
color blue, LdonPacc
#distance Fe_C20, (fep and name C20), (heme and name fe))

# The following 6 lines:
    # 1. Select non-hydro atoms of ligands
    # 2. Select protein atoms within 5A of selected atoms in last step
    # 3. Label alpha-c(ca) of selected residues with residue name and residue position
    # 4. Set label color back
    # 5. Set background white
    # 6. Hidden hydrogenes
select sele, indinavir & not hydro
select sele, byres (sele expand 5) & 1hsg
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',    \
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',    \
'GLY':'G', 'PRO':'P', 'CYS':'C'}
label name ca & sele, "%s-%s" % (one_letter[resn],resi)
bg white
set label_color, black
hide (hydro)

# The follwing 5 lines
    # 1. Comment out this line
    # 2. Create an object `surrounding_res` to represent selected protein atoms
    #    `create`: creates a new molecule object from a selection. It can also be used to create states in an   existing object.
    #    `create name, (selection)`
    # 3. Display created surface
    # 4. Set color for surrounding_res
    # 5. Set transparency for surrounding_res
    #    Transparency is used to adjust the transparency of Surfaces and Slices.    
    #    `set transparency, F, selection`
#show surface, 1hsg
create surrounding_res, sele
show surface, surrounding_res
color grey80, surrounding_res
set transparency, 0.5, surrounding_res

此外还可以使用如下脚本(list_hbonds.py)输出相互作用的原子及其位置。

# Copyright (c) 2010 Robert L. Campbell
from pymol import cmd

def list_hb(selection,selection2=None,cutoff=3.2,angle=55,mode=1,hb_list_name='hbonds'):
    """
    USAGE

    list_hb selection, [selection2 (default=None)], [cutoff (default=3.2)],
                       [angle (default=55)], [mode (default=1)],
                       [hb_list_name (default='hbonds')]

    The script automatically adds a requirement that atoms in the
    selection (and selection2 if used) must be either of the elements N or
    O.

    If mode is set to 0 instead of the default value 1, then no angle
    cutoff is used, otherwise the angle cutoff is used and defaults to 55
    degrees.

    e.g.
    To get a list of all H-bonds within chain A of an object
      list_hb 1abc & c. a &! r. hoh, cutoff=3.2, hb_list_name=abc-hbonds

    To get a list of H-bonds between chain B and everything else:
      list_hb 1tl9 & c. b, 1tl9 &! c. b

    """
    cutoff=float(cutoff)
    angle=float(angle)
    mode=float(mode)
    # ensure only N and O atoms are in the selection
    selection = selection + " & e. n+o"
    if not selection2:
        hb = cmd.find_pairs(selection,selection,mode=mode,cutoff=cutoff,angle=angle)
    else:
        selection2 = selection2 + " & e. n+o"
        hb = cmd.find_pairs(selection,selection2,mode=mode,cutoff=cutoff,angle=angle)

    # sort the list for easier reading
    hb.sort(lambda x,y:(cmp(x[0][1],y[0][1])))

    for pairs in hb:
        cmd.iterate("%s and index %s" % (pairs[0][0],pairs[0][1]), 'print "%1s/%3s`%s/%-4s " % (chain,resn,resi,name),')
        cmd.iterate("%s and index %s" % (pairs[1][0],pairs[1][1]), 'print "%1s/%3s`%s/%-4s " % (chain,resn,resi,name),')
        print "%.2f" % cmd.distance(hb_list_name,"%s and index %s" % (pairs[0][0],pairs[0][1]),"%s and index %s" % (pairs[1][0],pairs[1][1]))

#cmd.extend("list_hb",list_hb)
#if __name__ == "__main__":
cmd.load("E:/yunpan/docking/1hsg_prot.pdb", "1hsg")
cmd.h_add("(1hsg)")
cmd.load("E:/yunpan/docking/indinavir.pdbqt","indinavir")
cmd.h_add("(indinavir)")

h_donator  = "elem n,o & (neighbor hydro)"
h_acceptor = "elem o | (elem n & !(neighbor hydro))"

lacc = "indinavir & (elem o | (elem n & !(neighbor hydro)))"
ldon = "indinavir & (elem n,o & (neighbor hydro))"
pacc = "1hsg & (elem o | (elem n & !(neighbor hydro)))"
pdon = "1hsg & (elem n,o & (neighbor hydro))"

list_hb(ldon, pacc, hb_list_name="l2p_hbonds")
list_hb(lacc, pdon, hb_list_name="p2l_hbonds")

输出结果如下：

PyMOL>run E:/docking/list_hbonds.py
B/MK1`902/N4    B/GLY`27/O     3.03
B/MK1`902/O4    B/GLY`27/O     3.16
B/MK1`902/O2    A/ASP`25/OD1   2.77
B/MK1`902/O2    B/ASP`25/OD1   2.63

看上去比显示的氢键少了三个，这是因为我们在第二个函数中使用了H-键角度限制，如果在调用时给定参数list_hb(mode=0)则会获得一致结果。

H-bond结果展示。第一张图为运行display.pml后的结果，蓝色虚线为氢键；第二张图为运行list_hbonds.py后的结果, 黄色虚线为氢键（覆盖了之前的蓝色）。可以通过点选LaccPdon, LdonPacc, l2p_hbonds显示不同的氢键。

展示疏水表面

# 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)

将上面的脚本存储为color_h.py，在PyMOL界面运行File-Run-color_h.py，在命令行输入>PyMOl color_h- Show surface。