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 <tlinnet@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: 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 <tobiasbeck@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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