Parsing mmCIF files using Biopython

The mmCIF file format is probably the future. Biopython does not have yet full functionality to work with it, but we will take a look at what is here now.

Getting ready

As Bio.PDB is not able to automatically download mmCIF files, you need to get your protein file and rename it as 1tup.cif. This can be found at https://github.com/tiagoantao/bioinf-python/blob/master/notebooks/Datasets.ipynb under the 1TUP.cif name.

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

How to do it...

Take a look at the following steps:

1. Let's parse the file. We just use the mmCIF parser instead of the PDB parser:

   from __future__ import print_function
   from Bio import PDB
   parser = PDB.MMCIFParser()
   p53_1tup = parser.get_structure('P53', '1tup.cif')

2. Let's inspect the following chains:

   def describe_model(name, pdb):
       print()
       for model in p53_1tup:
           for chain in model:
               print('%s - Chain: %s. Number of residues: %d. Number of atoms: %d.' %
            ...