You should ask the Pymol devs. Have you tried setting PYTHONPATH before
running Pymol?
On 13 Jul 2016 5:55 p.m., "Thomas Ryckmans" <thomas.ryckm...@gmail.com>
wrote:
> Dear all,
>
> I am trying to install openbabel to run the Optimize plugin in Pymol (
> http://www.pymolwiki.org/index.php/Optimize).
> I installed the OpenBabelGUI 2.3.2
> I am using python 2.7 (Anaconda) with a 64 bit computer, so I I installed
> openbabel-1.8.4-cp27-none-win_amd64.whl, and the python bindings.
>
> It seems to work: I can follow the command lines here:
> and it works - e.g. these
>
> >>> import pybel
> >>> mol = pybel.readstring("smi", "CC(=O)Br")
> >>> mol.make3D()
> >>> print(mol.write("sdf"))
>
> give the expected output.
>
>
> However when I run pymol and try to use Optimize, I get the following
> error message:
> ---------------------------------------------------------------
> Error: 1
> <type 'exceptions.NameError'> Exception in Tk callback
> Function: <function set_conf_search at 0x0000000009CB02E8> (type: <type
> 'function'>)
> Args: ()
> Traceback (innermost last):
> File "C:\Program Files\PyMOL\\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py",
> line 1747, in __call__
> return apply(self.func, args)
> File "C:\Users\Thomas\AppData\Roaming\pymol\startup\optimize.py", line
> 52, in set_conf_search
> conf_search(selection, forcefield, conf_method, nsteps1, conformers,
> lowest_conf)
> File "C:\Users\Thomas\AppData\Roaming\pymol\startup\optimize.py", line
> 266, in conf_search
> obconversion = ob.OBConversion()
> <type 'exceptions.NameError'>: global name 'ob' is not defined
> ----------------------------------------------------------------
> I am assuming (...) that this is because pymol does not know where to find
> openbabel. How can I change that??
>
> In the openbabel directory, there is a file called babelconfig.h;
> containing these two lines:
> /* Where the data files are located */
> #define BABEL_DATADIR "C:/Program Files/openbabel/share/openbabel"
>
> while the data folder is actually elsewhere:
> C:\Users\Thomas\Anaconda2\Lib\site-packages\openbabel
>
> if I try to change the babelconfig.h file to
> /* Where the data files are located */
> #define BABEL_DATADIR
> "C:\Users\Thomas\Anaconda2\Lib\site-packages\openbabel"...
> nothing changes...
>
> many thanks for your help!
>
> Thomas
>
>
>
>
> ------------------------------------------------------------------------------
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------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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