[Biopython] Reading large files, Biopython cookbook example

[Katrina Lexa]

Hi everyone,

I'm trying to do something that seems like it ought to be super simple,
since it is on the Biopython wiki cookbook
(http://biopython.org/wiki/Reading_large_PDB_files), but for some reason
that script will not work for me. 

When I try to run it as it is, on a pdb file that has more than 10000
residues, I get the "NameError: global name 'Residue' is not defined" at
line 77. My assumption was that maybe the script needed to import some other
module from Biopython, so I added from Bio.PDB import * to the top of the
script, but then it failed with "TypeError: 'str' object is not callable" at
line 73 (residue = Residue(res_id, resname, self.segid). I tried to
circumvent this by just changing the name of the variable being created,
from residue = Residue to foobar = Residue (and then carrying that naming
through), but I continued to get the TypeError. Has anyone seen this before
and/or can anyone help me out getting this to run. 

I have a file where all of the residues after 9999 are numbered starting
with A000, and that causes the normal Bio.PDB.PDBParser to crash with
invalid literal for int() with base 10: 'A000', so if there is an easier
work around for that, that would also be a solution. 

Thank you so much for your help!