Some pdbs cannot be download from PDB using biopython, though they exist in PDB. It generates the error. This code is used to download pdb (2j8e) It could not download however it works for other pdbs.
Python 2.7.4 (default, May 14 2013, 09:41:12)
[GCC 4.4.6 20120305 (Red Hat 4.4.6-4)] on linux2
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>>> from Bio.PDB import PDBList
>>> pdbdownload = PDBList()
>>> pdbid = '2j8e'
>>> downloaded_path = pdbdownload.retrieve_pdb_file(pdbid)
Downloading PDB structure '2j8e'...
Traceback (most recent call last):
IOError: [Errno ftp error] [Errno ftp error] 550 Can't change directory to pdb2j8e.ent.gz: No such file or directory
This is an error. Has someone faced this problem?
I'm sorry, but that file doesn't exist! See by yourself:
ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/j8/
There are no pdb2j8e.ent.gz in that dir. If you try to download 2j8f or any other id, you get it without problem.
That file got obsolete, and can be retrieved from ftp://ftp.wwpdb.org/pub/pdb/data/structures/obsolete/pdb/j8/. With Biopython you can do:
downloaded_path = pdbdownload.retrieve_pdb_file(pdbid, obsolete=True)