I'm trying to separate RNA from protein in a complex protein/RNA PDB file and I want all RNA info with the hetero atoms in between the bases BUT without H20 etc. In short I want RNA part of pdb file without discontinuous lines.
I managed to separate RNA from protein with Bio PDB Select but it consider hetero atoms as amino acid when I use is_aa(residue). So hetero atoms wont appear in my "only RNA" file.
from Bio.PDB import *
from Bio.PDB import PDBParser, PDBIO, Select
import os
class ProtSelect(Select):
def accept_residue(self, residue):
return 1 if is_aa(residue) == True else 0
class RNASelect(Select):
def accept_residue(self, residue):
return 1 if is_aa(residue) == False and residue.id[0] != "W" else 0
pdb = PDBParser().get_structure("2bh2", "pdb2bh2.ent")
io = PDBIO()
io.set_structure(pdb)
io.save("seqprotest.pdb", ProtSelect())
io.save("seqRNAtest.pdb", RNASelect())
EDIT: I managed to do it:
class RNASelect(Select):
def accept_residue(self, residue):
return 1 if ((residue.id[0] != 'H_ MG') and ((residue.get_resname() == ' A' or residue.get_resname() == ' U' or residue.get_resname() == ' G' or residue.get_resname() == ' C' or residue.get_resname() == ' T') or (residue.id[0][0:2] == 'H_' and (residue.get_resname()[2] == 'U' or residue.get_resname()[2] == 'A' or residue.get_resname()[2] == 'C' or residue.get_resname()[2] == 'G' or residue.get_resname()[2] == 'T')))) else 0
It's not pretty but it do the job. The idea is to get everything that finish by a nucleotide. I figured out that hetatom's names of RNA chains always finish by a nucleotide letter so i just have to check everything that begins by 'H_' and ends by 'A,T,C,G,U'. Just remove 'H_ MG' and you're good.
