[Biopython-dev] Residue Depth class

[Giacomo Bastianelli]

Dear Biopython developers,

I am trying to use the ResidueDepth class.
I have installed the MSMS module and I get
this error:

Traceback (most recent call last):
File "test.py", line 8, in ?
  rd = ResidueDepth(model, '1SBC.pdb')
File "/usr/lib64/python2.3/site-packages/Bio/PDB/ResidueDepth.py", line 
132, in __init__
  surface=get_surface(pdb_file)
File "/usr/lib64/python2.3/site-packages/Bio/PDB/ResidueDepth.py", line 
83, in get_surface
  surface=_read_vertex_array(surface_file)
File "/usr/lib64/python2.3/site-packages/Bio/PDB/ResidueDepth.py", line 
51, in _read_vertex_array
  fp=open(filename, "r")
IOError: [Errno 2] No such file or directory: '/tmp/tmpEoynGC.vert'

I have python2.4 with biopython 1.43 in a linux ubuntu OS.

I checked the single programs (msms, pdb_to_xyzr)
and they seem to work fine.

this is the code that I use:
----------------------
from string import *
from Bio.PDB import *


parser = PDBParser()
structure = parser.get_structure('1SBC.pdb', '1SBC.pdb')
model = structure[0]
rd = ResidueDepth(model, '1SBC.pdb')
--------------------------

Thanks for your suggestions!

Giacomo