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 is here now.
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-Second-Edition/blob/master/Datasets.ipynb under the 1TUP.cif
name.
You can find this content in the Chapter07/mmCIF.ipynb
Notebook file.
Take a look at the following steps:
from Bio import PDB parser = PDB.MMCIFParser() p53_1tup = parser.get_structure('P53', '1tup.cif')
- 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.' % ...