Re: [PyMOL] apbs2 plugin failure
Did I say thanks? It seems I was using an older version of the plugin. The one downloaded just now works fine. Thanks! Andreas On 10/01/2013 9:18, Troels Emtekær Linnet wrote: 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 http://1.th 2300 København S Mobil: +45 60210234 -- 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/learnnow-d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] apbs2 plugin failure
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 docandr...@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 -- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] apbs2 plugin failure
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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
