Pymol（1.8.6）作图技巧之创建质心

一、首先，访问pymolwikiCenter of Mass，下载center_of_mass.py脚本；

或者把下面文件保存为center_of_mass.py文件。

See more here: http://www.pymolwiki.org/index.php/center_of_massDESCRIPTION   Places a pseudoatom at the center of mass   Author: Sean Law   Michigan State University   slaw (at) msu . eduSEE ALSO   pseudoatom, get_com'''from __future__ import print_functionfrom pymol import cmddef 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)# vi:expandtab:sw=3

二、将center_of_mass.py脚本放在pymol安装文件夹下的Lib文件夹。

三、创建质心操作

导入center of mass

import center_of_mass

创建质心球

修改质心球大小

set sphere_scale,0.4

创建质心的其他相关操作