I am having trouble with Biopyhton. I used this code to download a set of proteins
from Bio.PDB import *
from biopandas.pdb import PandasPdb
import Bio
from Bio.PDB import PDBList
ppdb0 = []
ppdb1 = []
pdbl = PDBList()
PDBlist2 = ['2dd6', '1lbO', 'iee7']
for i in PDBlist2:
ppdb0.append(pdbl.retrieve_pdb_file(i,pdir='.', file_format ='pdb'))
ppdb1.append(PandasPdb().fetch_pdb(i))
It was working pretty well but after restart my computer now I am having this error:
Downloading PDB structure '2dd6'...
Desired structure doesn't exists
Downloading PDB structure '1lbO'...
Desired structure doesn't exists
HTTP Error 404
Does anybody get the same? can you tell me how can I fix this, please? Pd: is the same if I use capital letters to write the protein accession number
By looking at the pages https://www.rcsb.org/structure/2DD6 and https://www.rcsb.org/structure/1lbO I can see: Protein 2DD6 does exist and returns a HTTP 200 result. A protein with ID 1lbO just does not exist so I get a 404 (page not found). And iee7 is not even a valid PDB ID as it does not start with a number. Protein 1EE7 does exist - Maybe a typo?