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
>>
>>
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