No output when trying to obtain protein sequence from PDB file
0
0
Entering edit mode
4.2 years ago
shome ▴ 10

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)
PDB biopython • 1.5k views
ADD COMMENT
0
Entering edit mode

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,

ADD REPLY
0
Entering edit mode

Not sure if this is the reason, but that particular structure file has no protein chains in it.

ADD REPLY
0
Entering edit mode

It is containing RNA structure.I want to get the RNA sequence out of it.

ADD REPLY

Login before adding your answer.

Traffic: 2628 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6