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
Troels Emtekær Linnet
Ved kløvermarken 9, 1.th
2300 København S
Mobil: +45 60210234
2013/1/3 Andreas Förster <[email protected]>
> 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
>
>
> ------------------------------------------------------------------------------
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
> MVPs and experts. ON SALE this month only -- learn more at:
> http://p.sf.net/sfu/learnmore_122712
> _______________________________________________
> PyMOL-users mailing list ([email protected])
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/[email protected]
>
------------------------------------------------------------------------------
Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
MVPs and experts. ON SALE this month only -- learn more at:
http://p.sf.net/sfu/learnmore_122712
_______________________________________________
PyMOL-users mailing list ([email protected])
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/[email protected]
