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Lecture 1: Applications of Python in Bioinformatics: Visualizing Protein (Python recipe) by Devashish Das
ActiveState Code (http://code.activestate.com/recipes/579050/)

This code reads 1qlz.pdb protein file can be downloaded from http://www.rcsb.org/pdb/files/1QLZ.pdb and plots a 3D graph using maplotlib library. For mystery write to me: devashish.das@educept.com

__author__  = Devashish Das
__contact__ = +91-9964218681
__email__   = deavshish.das@educept.com
__website__ = http://www.educept.com
Python, 29 lines
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#!/usr/bin/env python
#-*- coding:utf-8 -*-

__author__  = "Devashish Das"
__contact__ = "+91-9964218681"
__email__ = "deavshish.das@educept.com"

#http://www.educept.com

Store_all = []
with open("1qlz.pdb") as protein:
    for lines in protein:
        if "ATOM   " in lines:
            lines = lines.split()
            #'ATOM', '1', 'N', 'LEU', 'A', '125', '4.329', '-12.012', '2.376', '1.00', '0.00', 'N'
            Store_all.append(map(float, lines[6:9]))

import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D

x,y,z = zip(*Store_all)

fig = plt.figure()
ax = Axes3D(fig)

ax.plot(x,y,z, "o")
ax.axis("off")

plt.show()

Watch the video: https://youtu.be/GkadFs-igdQ

Tags: 3d, bioinformatics, plots, protein, python