[BioPython] Problem with Bio.PDB

[Shameer Khadar]

Hi,
I want to use Bio.PDB module to calculate HSE and Resdue depth for all
residues in a  couple of proteins.
This is the code I had written and am getting some serious errors :( .  (My
PyQ(Python Quotient is low, sorry if there is any significant syntax
errors:) ))
---
PS : Input PDB : http://www.rcsb.org/pdb/explore/explore.do?structureId=1crn
msms is installed on my computer.
--
1. HSE.py
_code_
#!/usr/bin/python
from Bio.PDB import *
parser = PDBParser()
structure = parser.get_structure('str1', '1crn.pdb')
model=structure[0]
hse = HSExposure()
exp_ca = hse.calc_hs_exposure(model, option='CA3')
exp_cb = hse.calc_hs_exposure(model, option='CB')
print exp_ca[100]
_error_
Traceback (most recent call last):
  File "HSE.py", line 12, in ?
    hse = HSExposure()
TypeError: 'module' object is not callable

2. rd.py
_code_
#!/usr/bin/python
from Bio.PDB import *
parser = PDBParser()
structure = parser.get_structure('str1', '1crn.pdb')
model=structure[0]
rd = ResidueDepth(model, '1crn.pdb')
residue_depth, ca_depth=rd[46]


_error_
pdb_to_xyzr: error, file 1crn.pdb line 91 residue    1 atom pattern THR N
was not found in ./atmtypenumbers
pdb_to_xyzr: error, file 1crn.pdb line 92 residue    1 atom pattern THR CA
was not found in ./atmtypenumbers
(..... till the last atom)
pdb_to_xyzr: error, file 1crn.pdb line 417 residue   46 atom pattern ASN OXT
was not found in ./atmtypenumbers
Traceback (most recent call last):
  File "rd.py", line 8, in ?
    rd = ResidueDepth(model, '1crn.pdb')
  File "/software/biopython-1.42/build/lib.linux-x86_64-2.3/Bio/PDB/ResidueDepth.py",
line 132, in __init__
    surface=get_surface(pdb_file)
  File "/software/biopython-1.42/build/lib.linux-x86_64-2.3/Bio/PDB/ResidueDepth.py",
line 83, in get_surface
    surface=_read_vertex_array(surface_file)
  File "/software/biopython-1.42/build/lib.linux-x86_64-2.3/Bio/PDB/ResidueDepth.py",
line 51, in _read_vertex_array
    fp=open(filename, "r")
--
Thanks
Shameer Khadar
NCBS-TIFR
Bangalore
India