No output when trying to obtain protein sequence from PDB file
I am trying to obtain the sequence from the PDB file, but no output is given when I run the following code :
from Bio import SeqIO
from Bio.PDB import *
import numpy as np
with open("1a9l.pdb", "r") as handle:
for record in SeqIO.parse(handle, "pdb-atom"):
print(record.seq)
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You don't need to open() something you pass to SeqIO. You can just pass the file itself to the parse function. I'm not sure if that is the problem here but it certainly won't be helping,
Not sure if this is the reason, but that particular structure file has no protein chains in it.
It is containing RNA structure.I want to get the RNA sequence out of it.