How can I use biopython to extract each alpha carbon from a PDB file?

I have a PDB file (2i0q.pdb), and I must extract the A chain from the PDB file to another file called "A.pdb" which I have already done successfully. Next, I have to take A.pdb and extract each alpha carbon ("CA") into another file. I have tried to write the function that does this, but my output file "CA.txt" appears to be blank. Can someone see what I have done wrong?

from Bio.PDB import *

parser=PDBParser()



structure=parser.get_structure('X', '2i0q.pdb')

#This extracts each chain in the PDB file into its own separate file
for chain in structure.get_chains():
    io.set_structure(chain)
    io.save(chain.get_id() + ".pdb")

structure_2 = parser.get_structure('Y', 'A.pdb')

def CA(structure):
    f = open('CA.txt', 'w')
    for atom in structure:
        if atom =='CA':
            f.write(atom)



CA(structure_2)

python biopython pdb

• 6,197 views • link

written 7.8 years ago by westin.kosater •

1 answer

I am sure there must be some other way to directly parse the structure(using Bio.PDB.PDBParser object) and get the records of the selected atom using Bio.PDB module.

But here I am directly parsing .pdb file and selecting the records of interest using the regular expression

from Bio.PDB import *
import re

parser=PDBParser()
io=PDBIO()
structure=parser.get_structure('X', '2i0q.pdb')

for chain in structure.get_chains():
    io.set_structure(chain)
    io.save(chain.get_id() + ".pdb")

## I am sure there must be some other way to directly parse the pdb structure and get the records of selected atom in Bio.PDB module.

def CA(pdbFileName):
    fw = open('CA.txt', 'w')
    fr = open(pdbFileName, 'r')

    for record in fr:
        if(re.search(r'^ATOM\s+\d+\s+CA\s+', record)):
            fw.write(record)

    fw.close()
    fr.close()

CA('A.pdb')

• 1 views • link

written 7.8 years ago by Nitin Narwade

This works. Thank you very much!

• 1 views • link

written 7.8 years ago by westin.kosater •