I'm beginner to python coding. I'm working over structural coordinates. I have pdb structure which have xyz coordinate information (last three col)
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
- I have 1000 atoms in my structure.
- I have two queries.
How I can calculate the centroid of the structure from xyz coordinates.
From the centroid I want to draw a sphere of radius 20cm.
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('
')
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
it gives the centroid of each atom (xyz) i need a central point how??????
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