Introducing Bio.PDB

Here, we will introduce Biopython's PDB module for working 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 Chapter07/PDB.ipynb Notebook file.

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 Bio import PDB

repository = PDB.PDBList()
repository.retrieve_pdb_file('1TUP', pdir='.', file_format='pdb')
repository.retrieve_pdb_file('1OLG', pdir...