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_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)
     
    
   

    

     

    
    

     

      
     
    
   

    

     

    
    

     

      # vi:expandtab:sw=3
     
    
  
 

三、创建质心操作

导入center of mass

import center_of_mass

修改质心球大小

set sphere_scale,0.4

创建质心的其他相关操作

文章来源: drugai.blog.csdn.net，作者：DrugAI，版权归原作者所有，如需转载，请联系作者。

原文链接：drugai.blog.csdn.net/article/details/77345827