title: How to Calculate Centroid in python
body: <p>I'm beginner to python coding. I'm working over structural coordinates. I have pdb structure which have xyz coordinate information (last three col)  </p>
  
  <pre><code>ATOM      1  N   SER A   1      27.130   7.770  34.390    
  ATOM      2  1H  SER A   1      27.990   7.760  34.930     
  ATOM      3  2H  SER A   1      27.160   6.960  33.790    
  ATOM      4  3H  SER A   1      27.170   8.580  33.790    
  ATOM      5  CA  SER A   1      25.940   7.780  35.250    
  ATOM      6  CB  SER A   1      25.980   9.090  36.020    
  ATOM      7  OG  SER A   1      26.740  10.100  35.320    
  ATOM      8  HG  SER A   1      26.750  10.940  35.860    
  ATOM      9  C   SER A   1      24.640   7.790  34.460    
  ATOM     10  O   SER A   1      24.530   8.510  33.500    
  ATOM     11  N   CYS A   2      23.590   7.070  34.760    
  ATOM     12  H   CYS A   2      23.590   6.550  35.610    
  ATOM     13  CA  CYS A   2      22.420   7.010  33.900    
  ATOM     14  CB  CYS A   2      21.620   5.760  34.270    
  ATOM     15  SG  CYS A   2      22.480   4.210  33.970    
  ATOM     16  C   CYS A   2      21.590   8.220  34.040    
  ATOM     17  O   CYS A   2      21.370   8.690  35.160   
  </code></pre>
  
  <ul>
  <li>I have 1000 atoms in my structure. </li>
  <li>I have two queries.</li>
  </ul>
  
  <p>How I can calculate the centroid of the structure from xyz coordinates.<br>
  From the centroid I want to draw a sphere of radius 20cm.    </p>
  
  <pre><code>I try this
  
  
  from __future__ import division
  import math as mean
  import numpy as nx
  from string import*
  
  
  infile = open('file.pdb', 'r')           #open my file
  text1 = infile.read().split('\n')
  infile.close()
  
  text = []
  for i in text1:
  if i != '':
      text.append(i)
  
  for j in text:
  x1 = eval(replace(j[30:38], ' ', ''))         #extract x-coordinate
  y1 = eval(replace(j[38:46], ' ', ''))         #extract y-coordinate
  z1 = eval(replace(j[46:54], ' ', ''))         #extract z-coordinate
  
  idcord = []
  idcord.append(x1); idcord.append(y1); idcord.append(z1)
  
  centroid = nx.mean(idcord)
  print centroid
  </code></pre>
  
  <p>it gives the centroid of each atom (xyz)
  i need a central point
  how??????</p>