Hi Andreas.

The line:
/usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py

shows that you are using the apbs tools from Michael G. Lerner.
http://pymolwiki.org/index.php/APBS

You might want to try out a little modified version of that.
http://pymolwiki.org/index.php/Apbsplugin

You might also want to try this.
That is the repository with all scripts from Pymolwiki, to work out of the box.
http://pymolwiki.org/index.php/Git_intro



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2013/1/3 Andreas Förster <docandreas@gmail.com>
Dear all,

on our RHEL computers (6.2, 64-bit) with PyMOL compiled from CVS, the
APBS2 plugin isn't functioning anymore.  The plugin window opens just
fine and the executables are found.

When I select "Use PDB2PQR" in the Main tab, clicking on Set grid
produces the following error:

Error: 1
<type 'exceptions.UnboundLocalError'> Exception in Tk callback
   Function: <function <lambda> at 0x7fc2b0705410> (type: <type 'function'>)
   Args: ()
Traceback (innermost last):
   File "/usr/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py",
line 1747, in __call__
     return apply(self.func, args)
   File
"/usr/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwDialog.py", line
153, in <lambda>
     command=lambda self=self, name=name: self._doCommand(name))
   File
"/usr/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwDialog.py", line
132, in _doCommand
     return command(name)
   File
"/usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py", line
1075, in execute
     self.runPsize()
   File
"/usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py", line
1096, in runPsize
     good = self.generatePqrFile()
   File
"/usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py", line
1007, in generatePqrFile
     good = self._generatePdb2pqrPqrFile()
   File
"/usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py", line
1615, in _generatePdb2pqrPqrFile
     if retval != 0:
<type 'exceptions.UnboundLocalError'>: local variable 'retval'
referenced before assignment

When I chose "User PyMOL generated PQR and PyMOL generated Hydrogens and
termini" or "User PyMOL generated PQR and existing hydrogens and
termini", I can set the grid, run APBS and visualize the result just fine.

I'm happy with that, but maybe someone has an idea of why the first
approach fails.


Thanks.


Andreas




--
         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
             http://www.msf.bio.ic.ac.uk

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