[Biopython] Shell permission denied

[Abel Valenzuela García]

Dear all,


I'm using Python 2.7.3 under Ubuntu 12.04 (precise pangolin). My best guess is that this has to do with the linux system, or its relationship with Python; it's very unlikely that the code is faulty.

At some point of my script execution, there is a system call to run a program from the linux shell that looks like this:

os.system("%s %s > %s" % (DSSP, in_file, out_file.name)) 
 This should basically run the command line

DSSP in_file > out_file

Here is the source code



The ERROR message I get (excerpt from my session):

In [8]: p = PDBParser()
In [9]: structure = p.get_structure("4E4Z", "4E4Z.pdb")
In [10]: model = structure[0]
In [11]: dssp = DSSP(model, "4E4Z.pdb")
sh: 1: dssp: Permission denied 

I followed the class documentation for that example, have
 a sane pdb file, a dssp package that works nicely and produces correct 
output from the command line, all permissions to execute, and I'm the only user.


Any ideas why this might not be working?




Thank you very much for you patience and help!


 


Abel Valenzuela
Bregnerødgade 20, 3 th
2200 Copenhagen N