Introduction

This tutorial describes how to use elastic network models, in particular Gaussian Network Model (GNM) and Anisotropic Network Model (ANM), for studying protein dynamics.

Required Programs

Latest version of ProDy and Matplotlib required.

Recommended Programs

IPython is highly recommended for interactive usage.

Getting Started

To follow this tutorial, you will need the following files:

 792 Feb 29 20:20 oanm_eigvals.txt
3.3M Feb 29 20:20 oanm_hes.txt
215K Feb 29 20:20 oanm_slwevs.txt
 91K Feb 29 20:20 ognm_kirchhoff.txt

We recommend that you will follow this tutorial by typing commands in an IPython session, e.g.:

$ ipython

or with pylab environment:

$ ipython --pylab

First, we will make necessary imports from ProDy and Matplotlib packages.

In [1]: from prody import *

In [2]: from pylab import *

In [3]: ion()

We have included these imports in every part of the tutorial, so that code copied from the online pages is complete. You do not need to repeat imports in the same Python session.