Introducing Bio.PDB

Here, we will introduce Biopython's PDB module to deal with the Protein Data Bank. We will use three models that represent part of the p53 protein. You can read more about these files and p53 at http://www.rcsb.org/pdb/101/motm.do?momID=31.

Getting ready

You should be aware of the basic PDB data model of Model/Chain/Residue/Atom objects. A good explanation on Biopython's Structural Bioinformatics FAQ can be found at http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ.

You can find this content in the 06_Prot/PDB.ipynb notebook.

Of the three models that we will download, the 1TUP model will be used in the remaining recipes. Take some time to study this model as it will help you later on.

How to do it...

Take a look at the following steps:

1. First, let's retrieve our models of interest as follows:

   from __future__ import print_function
   from Bio import PDB
   repository = PDB.PDBList()
   repository.retrieve_pdb_file('1TUP', pdir='.')
   repository.retrieve_pdb_file('1OLG...