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Bioinformatics with Python Cookbook by Tiago Antao

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Computing molecular distances on a PDB file

Here, we will find atoms closer to three zincs on the 1TUP model. We will consider several distances to these zincs. We will take this opportunity to discuss the performance of algorithms.

Getting ready

You can find this content in the 06_Prot/Distance.ipynb notebook. Take a look at the Bio.PDB recipe.

How to do it...

Take a look at the following steps:

  1. Let's load our model as follows:
    from __future__ import print_function
    from Bio import PDB
    repository = PDB.PDBList()
    parser = PDB.PDBParser()
    repository.retrieve_pdb_file('1TUP', pdir='.')
    p53_1tup = parser.get_structure('P 53', 'pdb1tup.ent')
  2. We will now get our zincs against which we perform later comparisons:
    zns = [] for atom in p53_1tup.get_atoms(): if ...

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