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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