Parsing mmCIF files using Biopython

The mmCIF file format is probably the future. Biopython doesn’t have full functionality to work with it yet, but we will take a look at what currently exists.

Getting ready

As Bio.PDB is not able to automatically download mmCIF files, you need to get your protein file and rename it to 1tup.cif. This can be found at https://github.com/PacktPublishing/Bioinformatics-with-Python-Cookbook-third-Edition/blob/master/Datasets.py under 1TUP.cif.

You can find this content in the Chapter08/mmCIF.py Notebook file.

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 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:
     ...