pymol作图-ΠΠ堆叠

利用pymol画出ΠΠ堆叠效果图以及距离：
在这之前要在pymol下面放一个名为center_of_mass.py的脚本，或者复制下面命令行保存成center_of_mass.py也可以。
关于放脚本的文件夹：我是用conda安装python38环境，center_of_mass.py放到 path\anaconda\envs\python38\Lib 下即可

'''
See more here: http://www.pymolwiki.org/index.php/center_of_mass

DESCRIPTION

   Places a pseudoatom at the center of mass

   Author: Sean Law
   Michigan State University
   slaw (at) msu . edu

SEE ALSO

   pseudoatom, get_com
'''

#from __future__ import print_function
from pymol import cmd


def com(selection, state=None, mass=None, object=None, quiet=1, **kwargs):
    quiet = int(quiet)
    if (object == None):
        try:
            object = cmd.get_legal_name(selection)
            object = cmd.get_unused_name(object + "_COM", 0)
        except AttributeError:
            object = 'COM'
    cmd.delete(object)

    if (state != None):
        x, y, z = get_com(selection, mass=mass, quiet=quiet)
        if not quiet:
            print("%f %f %f" % (x, y, z))
        cmd.pseudoatom(object, pos=[x, y, z], **kwargs)
        cmd.show("spheres", object)
    else:
        for i in range(cmd.count_states()):
            x, y, z = get_com(selection, mass=mass, state=i + 1, quiet=quiet)
            if not quiet:
                print("State %d:%f %f %f" % (i + 1, x, y, z))
            cmd.pseudoatom(object, pos=[x, y, z], state=i + 1, **kwargs)
            cmd.show("spheres", 'last ' + object)

cmd.extend("com", com)


def get_com(selection, state=1, mass=None, quiet=1):
    """
 DESCRIPTION

    Calculates the center of mass

    Author: Sean Law
    Michigan State University
    slaw (at) msu . edu
    """
    quiet = int(quiet)

    totmass = 0.0
    if mass != None and not quiet:
        print("Calculating mass-weighted COM")

    state = int(state)
    model = cmd.get_model(selection, state)
    x, y, z = 0, 0, 0
    for a in model.atom:
        if (mass != None):
            m = a.get_mass()
            x += a.coord[0] * m
            y += a.coord[1] * m
            z += a.coord[2] * m
            totmass += m
        else:
            x += a.coord[0]
            y += a.coord[1]
            z += a.coord[2]

    if (mass != None):
        return x / totmass, y / totmass, z / totmass
    else:
        return x / len(model.atom), y / len(model.atom), z / len(model.atom)

cmd.extend("get_com", get_com)

1. 如下图所示，假设49PRO、50TRP两个残基有ΠΠ相互作用，想作图观看
   
2. 任意选择每个环两个相对的原子，定义该环的几何中心

# 输入命令
import center_of_mass
com sele, object=p1	# 点击49PRO，环上相对的两个原子
com sele, object=p2	# 点击50TRP，环1上相对的两个原子
com sele, object=p3	# 点击50TRP，环2上相对的两个原子
set sphere_scale ,0.3		# 调节球的大小

注意图中右下角红框内，Selecting Atoms 才是选择原子

3. 点击菜单栏 Wizard > Measurement， 在右下角出现Measurement，分别点击两个球就能得到两个环之心间的距离，距离的数值也会给出。
点击50TRP、49pro一栏中 L > residue (one letter)，会出现残基缩写+残基序号；
注意右下角Mouse Mode 3-Butoon Editing，出现Editing时，按住Ctrl + 鼠标左键，可以移动距离数值（4.8，5.8）以及残基缩写+残基序号，让图片更美观；
做完后点击Measurement 下面的done，以及点击 Mouse Mode 3-Butoon Editing，改成 Mouse Mode 3-Butoon Viewing

4. 出图
输入下面命令得到下图：

bg_color white		#背景颜色调成白色
ray
png inter.png, 16.93cm, 16.93cm, dpi=300
save hbond.png