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)