Hi Troels,
Many thanks for your email!
I found a work around for my problem this morning: I copied the pdb2pqr
directory from my Mac and now the plugin works. I guess for the Ubuntu
pymol package, the pdb2pqr is not installed by default?
>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
Yes, I have also tried to use svn this morning, but got same error.
Thanks again!
Best wishes, Tobias.
On Mon, Jun 3, 2013 at 11:28 AM, Troels Emtekær Linnet <tlin...@gmail.com>wrote:
> 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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