From: Thomas J. <jue...@gm...> - 2007-12-18 02:03:16
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Dear all, when trying to use the APBS plugin I experience the following problem The first time I tried to run it it the error message was simply "ObjectMapLoadDXFile-Error: Unable to open file!" Now the second time it pops up an error log: Error: 1 WindowsError Exception in Tk callback Function: <bound method PmwFileDialog.okbutton of <pmg_tk.startup.apbs_tools.PmwFileDialog instance at 0x05961A30>> (type: <type 'instancemethod'>) Args: () Traceback (innermost last): File "d:\Program Files\DeLano Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "d:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\apbs_tools.py", line 1711, in okbutton self.setfilename(fn) File "d:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\apbs_tools.py", line 1745, in setfilename self.configure(directory=dir,filename=value) File "d:\Program Files\DeLano Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py", line 729, in configureapbs.exe func() File "d:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\apbs_tools.py", line 1769, in newdir self.fillit() File "d:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\apbs_tools.py", line 1836, in fillit fl=os.listdir(dir) WindowsError: [Errno 123] The filename, directory name, or volume label syntax is incorrect: 'd:APBS-0.5.1\\bin\\d:APBS-0.5.1\\bin/*.*' Both pymol (1.0edu1) and apbs (0.5.1)are fresh and clean installations. APBS is installed in D:\APBS-0.5.1 I experienced similiar problems on another Windows machine and a Mac, but both without the error log above. I was realizing that when choosing the location of APBS binary pymol writes: d:APBS-0.5.1 where it should be d:\APBS-0.5.1 I tried to put the correct path manually d:\APBS-0.5.1\bin\apbs.exe, but did not help. Any suggestions? Many thanks, Thomas |
From: Chen Z. <che...@gm...> - 2013-06-18 02:36:40
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Dear Pymol Users, I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian Wheezy machine. The initialization is successful, but when I hit "set grid", I got the error message below: *error: 1 <type 'exceptions.UnboundLocalError'> Exception in Tk callback Function: <function <lambda> at 0x33a6938> (type: <type 'function'>) Args: () Traceback (innermost last): File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", line 153, in <lambda> command=lambda self=self, name=name: self._doCommand(name)) File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", line 132, in _doCommand return command(name) File "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line 1075, in execute self.runPsize() File "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line 1096, in runPsize good = self.generatePqrFile() File "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line 1007, in generatePqrFile good = self._generatePdb2pqrPqrFile() File "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line 1615, in _generatePdb2pqrPqrFile if retval != 0: <type 'exceptions.UnboundLocalError'>: local variable 'retval' referenced before assignment* Also, although I specified the PATH of APBS and PDB2PQR in apbs_tools.py file, the APBS GUI in pymol is still unable to show the correct path of APBS and PDB2PQR. Thank you so much! Sincerely, Chen |
From: Troels E. L. <tl...@gm...> - 2013-06-18 05:40:42
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Have a look on the earlier message on this. http://www.mail-archive.com/pym...@li.../msg11148.html Troels Emtekær Linnet 2013/6/18 Chen Zhao <che...@gm...> > Dear Pymol Users, > > I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian > Wheezy machine. The initialization is successful, but when I hit "set > grid", I got the error message below: > > *error: 1 > <type 'exceptions.UnboundLocalError'> Exception in Tk callback > Function: <function <lambda> at 0x33a6938> (type: <type 'function'>) > Args: () > Traceback (innermost last): > File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line > 1747, in __call__ > return apply(self.func, args) > File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", > line 153, in <lambda> > command=lambda self=self, name=name: self._doCommand(name)) > File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", > line 132, in _doCommand > return command(name) > File > "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line > 1075, in execute > self.runPsize() > File > "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line > 1096, in runPsize > good = self.generatePqrFile() > File > "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line > 1007, in generatePqrFile > good = self._generatePdb2pqrPqrFile() > File > "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line > 1615, in _generatePdb2pqrPqrFile > if retval != 0: > <type 'exceptions.UnboundLocalError'>: local variable 'retval' referenced > before assignment* > > Also, although I specified the PATH of APBS and PDB2PQR in apbs_tools.py > file, the APBS GUI in pymol is still unable to show the correct path of > APBS and PDB2PQR. > > Thank you so much! > > Sincerely, > Chen > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: Chen Z. <che...@gm...> - 2013-06-18 12:23:01
|
Thank you so much Troels, This solves my problem. But based on this, it seems that APBS In pymol failed to find PDB2PQR. Chen On Tue, Jun 18, 2013 at 1:40 AM, Troels Emtekær Linnet <tl...@gm...>wrote: > Have a look on the earlier message on this. > > http://www.mail-archive.com/pym...@li.../msg11148.html > > > > Troels Emtekær Linnet > > > 2013/6/18 Chen Zhao <che...@gm...> > >> Dear Pymol Users, >> >> I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian >> Wheezy machine. The initialization is successful, but when I hit "set >> grid", I got the error message below: >> >> *error: 1 >> <type 'exceptions.UnboundLocalError'> Exception in Tk callback >> Function: <function <lambda> at 0x33a6938> (type: <type 'function'>) >> Args: () >> Traceback (innermost last): >> File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", >> line 1747, in __call__ >> return apply(self.func, args) >> File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", >> line 153, in <lambda> >> command=lambda self=self, name=name: self._doCommand(name)) >> File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", >> line 132, in _doCommand >> return command(name) >> File >> "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line >> 1075, in execute >> self.runPsize() >> File >> "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line >> 1096, in runPsize >> good = self.generatePqrFile() >> File >> "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line >> 1007, in generatePqrFile >> good = self._generatePdb2pqrPqrFile() >> File >> "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line >> 1615, in _generatePdb2pqrPqrFile >> if retval != 0: >> <type 'exceptions.UnboundLocalError'>: local variable 'retval' referenced >> before assignment* >> >> Also, although I specified the PATH of APBS and PDB2PQR in apbs_tools.py >> file, the APBS GUI in pymol is still unable to show the correct path of >> APBS and PDB2PQR. >> >> Thank you so much! >> >> Sincerely, >> Chen >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Windows: >> >> Build for Windows Store. >> >> http://p.sf.net/sfu/windows-dev2dev >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > |
From: Troels E. L. <tl...@gm...> - 2013-06-18 15:09:15
|
Do you have linux or windows? Do you have PDB2PQR on your system? http://pymolwiki.org/index.php/Apbsplugin http://www.poissonboltzmann.org/pdb2pqr Troels Emtekær Linnet 2013/6/18 Chen Zhao <che...@gm...> > Thank you so much Troels, > > This solves my problem. But based on this, it seems that APBS In pymol > failed to find PDB2PQR. > > Chen > > > On Tue, Jun 18, 2013 at 1:40 AM, Troels Emtekær Linnet <tl...@gm...>wrote: > >> Have a look on the earlier message on this. >> >> >> http://www.mail-archive.com/pym...@li.../msg11148.html >> >> >> >> Troels Emtekær Linnet >> >> >> 2013/6/18 Chen Zhao <che...@gm...> >> >>> Dear Pymol Users, >>> >>> I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian >>> Wheezy machine. The initialization is successful, but when I hit "set >>> grid", I got the error message below: >>> >>> *error: 1 >>> <type 'exceptions.UnboundLocalError'> Exception in Tk callback >>> Function: <function <lambda> at 0x33a6938> (type: <type 'function'>) >>> Args: () >>> Traceback (innermost last): >>> File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", >>> line 1747, in __call__ >>> return apply(self.func, args) >>> File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", >>> line 153, in <lambda> >>> command=lambda self=self, name=name: self._doCommand(name)) >>> File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", >>> line 132, in _doCommand >>> return command(name) >>> File >>> "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line >>> 1075, in execute >>> self.runPsize() >>> File >>> "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line >>> 1096, in runPsize >>> good = self.generatePqrFile() >>> File >>> "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line >>> 1007, in generatePqrFile >>> good = self._generatePdb2pqrPqrFile() >>> File >>> "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line >>> 1615, in _generatePdb2pqrPqrFile >>> if retval != 0: >>> <type 'exceptions.UnboundLocalError'>: local variable 'retval' >>> referenced before assignment* >>> >>> Also, although I specified the PATH of APBS and PDB2PQR in apbs_tools.py >>> file, the APBS GUI in pymol is still unable to show the correct path of >>> APBS and PDB2PQR. >>> >>> Thank you so much! >>> >>> Sincerely, >>> Chen >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF.net email is sponsored by Windows: >>> >>> Build for Windows Store. >>> >>> http://p.sf.net/sfu/windows-dev2dev >>> _______________________________________________ >>> PyMOL-users mailing list (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >>> >> >> > |
From: Troels E. L. <tl...@gm...> - 2013-06-18 15:26:15
|
Hi Chen. If you are up for it, pdb2pqr exist in the Pymol-script repo. http://pymolwiki.org/index.php/Git I have made a automatic compile script. See here: http://pymolwiki.org/index.php/User:Tlinnet/Linux_Install#Install_script That should fix it for you. Try to look it through, and just write if you have problems. Troels Emtekær Linnet 2013/6/18 Chen Zhao <che...@gm...> > I am using Debian linux and I installed PDB2PQR with path specified in > pymol APBS GUI. However, it seems that there are some problems in python, > although I don't understand because I am not a programmer. I will try to > run from command line instead. > > Thank you! > > Chen > > > On Tue, Jun 18, 2013 at 11:08 AM, Troels Emtekær Linnet <tl...@gm... > > wrote: > >> Do you have linux or windows? >> >> Do you have PDB2PQR on your system? >> http://pymolwiki.org/index.php/Apbsplugin >> http://www.poissonboltzmann.org/pdb2pqr >> >> >> Troels Emtekær Linnet >> >> >> 2013/6/18 Chen Zhao <che...@gm...> >> >>> Thank you so much Troels, >>> >>> This solves my problem. But based on this, it seems that APBS In pymol >>> failed to find PDB2PQR. >>> >>> Chen >>> >>> >>> On Tue, Jun 18, 2013 at 1:40 AM, Troels Emtekær Linnet < >>> tl...@gm...> wrote: >>> >>>> Have a look on the earlier message on this. >>>> >>>> >>>> http://www.mail-archive.com/pym...@li.../msg11148.html >>>> >>>> >>>> >>>> Troels Emtekær Linnet >>>> >>>> >>>> 2013/6/18 Chen Zhao <che...@gm...> >>>> >>>>> Dear Pymol Users, >>>>> >>>>> I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a >>>>> Debian Wheezy machine. The initialization is successful, but when I hit >>>>> "set grid", I got the error message below: >>>>> >>>>> *error: 1 >>>>> <type 'exceptions.UnboundLocalError'> Exception in Tk callback >>>>> Function: <function <lambda> at 0x33a6938> (type: <type 'function'>) >>>>> Args: () >>>>> Traceback (innermost last): >>>>> File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", >>>>> line 1747, in __call__ >>>>> return apply(self.func, args) >>>>> File >>>>> "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", line 153, >>>>> in <lambda> >>>>> command=lambda self=self, name=name: self._doCommand(name)) >>>>> File >>>>> "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", line 132, >>>>> in _doCommand >>>>> return command(name) >>>>> File >>>>> "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line >>>>> 1075, in execute >>>>> self.runPsize() >>>>> File >>>>> "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line >>>>> 1096, in runPsize >>>>> good = self.generatePqrFile() >>>>> File >>>>> "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line >>>>> 1007, in generatePqrFile >>>>> good = self._generatePdb2pqrPqrFile() >>>>> File >>>>> "/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", line >>>>> 1615, in _generatePdb2pqrPqrFile >>>>> if retval != 0: >>>>> <type 'exceptions.UnboundLocalError'>: local variable 'retval' >>>>> referenced before assignment* >>>>> >>>>> Also, although I specified the PATH of APBS and PDB2PQR in >>>>> apbs_tools.py file, the APBS GUI in pymol is still unable to show the >>>>> correct path of APBS and PDB2PQR. >>>>> >>>>> Thank you so much! >>>>> >>>>> Sincerely, >>>>> Chen >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> This SF.net email is sponsored by Windows: >>>>> >>>>> Build for Windows Store. >>>>> >>>>> http://p.sf.net/sfu/windows-dev2dev >>>>> _______________________________________________ >>>>> PyMOL-users mailing list (PyM...@li...) >>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>> Archives: >>>>> http://www.mail-archive.com/pym...@li... >>>>> >>>> >>>> >>> >> > |