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 <chenzhaoh...@gmail.com>
> 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
> <tlin...@gmail.com>wrote:
>
>> Have a look on the earlier message on this.
>>
>>
>> http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11148.html
>>
>>
>>
>> Troels Emtekær Linnet
>>
>>
>> 2013/6/18 Chen Zhao <chenzhaoh...@gmail.com>
>>
>>> 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 (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
>>>
>>
>>
>
------------------------------------------------------------------------------
This SF.net email is sponsored by Windows:
Build for Windows Store.
http://p.sf.net/sfu/windows-dev2dev
_______________________________________________
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
