[Biopython] running naccess

[Peter]

On Wed, Jul 21, 2010 at 3:51 PM, Bala subramanian
<bala.biophysics at gmail.com> wrote:
> Friends,
> I am trying to run naccess as follows.
>
> from Bio.PDB.PDBParser import PDBParser
> par = PDBParser()
> structure = par.get_structure('test','12_25.pdb')
> import Bio.PDB.NACCESS as nac
> data=nac.run_naccess(structure[0],'12_25.pdb')
>
> It seems that there is an issue with tmp dir creation. I could nt run
> naccess even if i define *temp_path='.'* with run_naccess function. Kindly
> write me how to resolve the issue.
>
>
> *I get the following error:*
>
> IOError                                   Traceback (most recent call last)
>
> /tmp/tmpqQLhRl/<ipython console> in <module>()
>
> /apps/py_modules/gcc/lib/python2.6/site-packages/Bio/PDB/NACCESS.pyc in
> run_naccess(model, pdb_file, probe_size, z_slice, naccess, temp_path)
>     56     # get the output, then delete the temp directory
>
>     57     rsa_file = tmp_pdb_file[:-4] + '.rsa'
> ---> 58     rf = open(rsa_file)
>     59     rsa_data = rf.readlines()
>     60     rf.close()
>
> IOError: [Errno 2] No such file or directory: '/tmp/tmpqQLhRl/tmpaOkRlK.rsa'

Try putting some debug print statements into NACCESS.py, in
particular see what stdout and stderr contain. My guess is there
is a problem running the tool.

Also try running the NACCESS command line tool by hand at
the command prompt, to make sure it is installed and working
correctly.

Peter