The x, y, and z coordinates of atoms are provided in the PDB file. One way to extract them is by using the Biopython package [1]. In this article, we will extract coordinates of C-alpha atoms for each residue from the PDB file using Biopython.

Let’s say we have a PDB file named ‘input.pdb‘.

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#!/usr/bin/env python3

from Bio.PDB import *
import numpy as np

p=PDBParser()

structure=p.get_structure('input', "input.pdb")

for model in structure:
      for chain in model:
            CA_coord = []
            for residue in chain:
                CA_coord.append((residue['CA'].get_vector()))
                print(CA_coord)

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Save this file as Python script, for example, as ‘ca_coord.py‘, keep your input file in the same directory or provide the full path in the script, and run it as:

python3 ca_coord.py

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References

1. https://biopython.org/