I'm currently using pymol's iterate to get all the residue numbers, and then I use those to retrieve the residue name. I don't think that's the best way to do it. I tried to look for a way in biopython to no avail. I would appreciate your input and suggestions.
A side question, sometimes even chain[i].resname gives me a KeyError: ('', 'number', '') with a certain residue, which made me use a try and except block. Any alternatives?
from Bio import *from Bio.PDB.PDBParser import PDBParserfrom Bio.PDB.Polypeptide import PPBuilderstructure = PDBParser().get_structure('5bmy', '5bmy.pdb') model = structure[0]chain = model['A']import __main____main__.pymol_argv = ['pymol','-qc']import pymolfrom pymol import cmd, storedpymol.finish_launching()cmd.load('5bmy.pdb') # use the name of your pdb filestored.residues = []cmd.iterate('name ca', 'stored.residues.append(resi)')numbers = [ int(x) for x in stored.residues ]for i in numbers: print (chain[i].resname)
