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POHow to Calculate Centroid in python
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copied!<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>

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