retrieve_pdb_file from Bio.PDB.PDBList creates .ent files, not .pdb

Question

[Maya]

I'm using Biopython to load structures into my code. I then change them into poses, via PyRosetta, because I want to align my theo structure to the PDB website structures. This is my code:

pdbl = PDBList()
native_pdb = pdbl.retrieve_pdb_file('%s' %protein, pdir='/Users/mlane/PyRosetta4/test_natives', file_format='pdb')
native_pose = pose_from_pdb(native_pdb)

but the retrieve_pdb_file creates .ent files and not pdb files. how do I fix this?

OR how do I load the known PDB structures in order to align them to theo structures and find the rmsd?

[Maya]

I still can't solve this issue. Does anybody know why retrieve_pdb_file isn't working correctly? Is anybody experiencing the same issue?

Answer 1

[Mensur Dlakic]

Most likely there is no need to fix anything. If you open the .ent files in a text editor they should look like PDB files. Simply change the file extension if it is important that they end in .pdb.

[Maya]

Okay, I'll try that. thank you! it matters for the next line "pose_from_pdb()" is an object that only accepts pdb files.

[Maya]

That didn't work, but thank you for your help!

[Mensur Dlakic]

What is it that didn't work?

I just ran this short script:

from Bio.PDB.PDBList import PDBList
pdbl = PDBList()
native_pdb = pdbl.retrieve_pdb_file('1ako', pdir='./', file_format='pdb')

It downloaded a file named pdb1ako.ent, which IS in PDB format, even though it ends in .ent. Simply running mv pdb1ako.ent 1ako.pdb would give a file in a proper format and with .pdb extension.