How to extract x,y,z coordinates of atoms from PDB file?

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‘.

#!/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)

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

References

1. https://biopython.org/