Hej Tobias.
Some time ago, a year+?, I played around fixing some small things in APBS,
to make it easier to work. (Most fixing small path things)
Orginal version:
http://pymolwiki.org/index.php/APBS
Small modified version:
http://pymolwiki.org/index.php/Apbsplugin
The modified version, is packed into the Pymol-script-repo
http://pymolwiki.org/index.php/Git
I made this installation script some time ago,
http://www.pymolwiki.org/index.php/User:Tlinnet/Linux_Install#Install_script
which download the Pymol-script-repo, and sets the path right.
at the moment I can't test it? since:
svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
svn: E210002: Unable to connect to a repository at URL 'svn://
svn.code.sf.net/p/pymol/code/trunk/pymol'
svn: E210002: Network connection closed unexpectedly
But maybe you can see from the script, what you have to do.
Best
Troels Emtekær Linnet
2013/5/31 Tobias Beck <tobiasb...@gmail.com>:
> Dear all,
>
> I am trying to run the ABPS plugin with PyMOL Version 1.6.0.0 on Ubuntu
> 12.10. I have compiled pymol from source
> (http://www.pymolwiki.org/index.php/Linux_Install).
>
> When running the plugin, I can set the grid, but after clicking on Run
APBS,
> I get the following error:
>
> Unexpected error: (<type 'exceptions.ImportError'>, ImportError('No module
> named pdb2pqr.pdb2pqr',), <traceback object at 0x7fd130771200>)
> <type 'exceptions.UnboundLocalError'> Exception in Tk callback
> Function: <function <lambda> at 0x7fd13078e398> (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 "/home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py", line 1036,
in
> execute
> good = self.generatePqrFile()
> File "/home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py", line 1007,
in
> generatePqrFile
> good = self._generatePdb2pqrPqrFile()
> File "/home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py", line 1615,
in
> _generatePdb2pqrPqrFile
> if retval != 0:
> <type 'exceptions.UnboundLocalError'>: local variable 'retval' referenced
> before assignment
>
> The first line suggests that the pdb2pqr module cannot be loaded. However,
> the grid seems to be set okay. Has anybody encountered this error before
and
> knows how to solve it?
>
> I have also tried the pymol version that can be installed with apt-get,
but
> same error.
>
> Thanks for any advice!
>
> Best wishes, Tobias.
>
>
>
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