This tutorial shows how to use the ANM to analyze the motions of proteins in the presence of membranes.

Required Programs

The latest version of ProDy is required for calculations, and the latest version of VMD is required for visualization.

Getting Started

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

 7.5K May 10 09:33 2nwl_blocks.txt
1008K May 10 09:33 2NWL-opm.pdb
 7.6K May 10 09:33 3kbc_blocks.txt
 1.1M May 10 09:33 3KBC-opm.pdb

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.