Thanks Noel - looking at the PyMol Mailing list, it looks like this already
happened... and the author of the post concludes this is an Open Babel
issue, not a Pymol issue :-)
https://sourceforge.net/p/pymol/mailman/message/33031324/
Will try again tonight...
many thanks
Thomas
On 15 July 2016 at 14:41, Noel O'Boyle <baoille...@gmail.com> wrote:
> (please cc the list)
>
> When I said the command prompt, I meant the Windows command prompt.
> PYTHONPATH is an environment variable.
>
> You really should contact the author of the plugin at this point - he
> can easily tell you how to do it.
>
> - Noel
>
> On 14 July 2016 at 17:59, Thomas Ryckmans <thomas.ryckm...@gmail.com>
> wrote:
> > Hi Noel,
> >
> > I ran the sys.path.append... when I type pymol in the command line I get
> >
> >>>> Pymol
> > Traceback (most recent call last):
> > File "<stdin>", line 1, in <module>
> > NameError: name 'Pymol' is not defined
> >
> > Yet I have installed pymol (from a .msi: EduPyMOL-v1.7.4.5-Win64)
> >
> > If I run pymol (I use the "C:\Program Files\PyMOL\PyMOL\PymolWin.exe"
> -J), I
> > can use the python command line...
> >
> > is there another installer that would give me a pymol.py file??
> >
> > many thanks
> >
> > Thomas
> >
> > On 14 July 2016 at 07:55, Noel O'Boyle <baoille...@gmail.com> wrote:
> >>
> >> Just try setting the PYTHONPATH at the command line before running Pymol
> >> at the same command line.
> >>
> >> On 13 Jul 2016 9:54 p.m., "Thomas Ryckmans" <thomas.ryckm...@gmail.com>
> >> wrote:
> >>>
> >>> Hi Noel,
> >>>
> >>> thank you so much for your comment - I am a newbie and very much stuck.
> >>> I tried both
> >>>
> >>> import sys
> >>>
> >>>
> sys.path.append("C:\Users\Thomas\Anaconda2\Lib\site-packages\openbabel\data")
> >>> print sys.path
> >>>
> >>> import sys
> >>>
> sys.path.append("C:\Users\Thomas\Anaconda2\Lib\site-packages\openbabel")
> >>> print sys.path
> >>>
> >>> but I still get an error message:
> >>>
> >>> Error: 1
> >>> <type 'exceptions.NameError'> Exception in Tk callback
> >>> Function: <function set_conf_search at 0x00000000031FA2E8> (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
> >>>
> >>> any ideas of what I should do next??
> >>>
> >>> Thomas
> >>>
> >>> On 13 July 2016 at 21:28, Noel O'Boyle <baoille...@gmail.com> wrote:
> >>>>
> >>>> 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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> >>>>>
> >>>
> >
>
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