Re: [PyMOL] Pymol error

[Rhitankar P. <rhi...@gm...>]

Dear Thomas,

Thanks for the informations. I think I am able to use port to install the
pymol1.5 version but I would also need to remove the existing 1.6 version.
Can you tell me the command to uninstall the existing version and then do a
fresh installation?

Thanks again
Rhitankar






On Wed, May 8, 2013 at 12:34 PM, Thomas Holder <
tho...@sc...> wrote:

> Dear Rhitankar,
>
> I should point out that Schrödinger also sells pre-compiled PyMOL with
> easy to use installers. http://pymol.org/academic.html
>
> Open-Source PyMOL was always targeted to power-users who are familiar
> with compiling software themselves.
>
> Regarding your question: It will most likely not be possible to compile
> and install open-source PyMOL with the system python on Mac, because OSX
> ships with an incompatible Tkinter library. So Pmw won't be your last
> problem.
>
> With macports it should work fine if you do this (see also David's
> answers):
>
> sudo port install tcl -corefoundation +threads
> sudo port install tk -quartz +x11
> sudo port install pymol
>
> Hope that helps.
>
> Cheers,
>   Thomas
>
> Rhitankar Pal wrote, On 05/08/13 18:01:
> > Dear Thomas,
> >
> > Even after I installed the Pmw1.3 which should be compatible with
> > python2.7 and reinstalling the pymol, I am still the following error
> > message.
> >
> >   File "/Library/Python/2.7/site-packages/pymol/__init__.py", line 450,
> > in launch_gui
> >     __import__(self.invocation.options.gui)
> >   File "/Library/Python/2.7/site-packages/pmg_tk/__init__.py", line 22,
> > in <module>
> >     from PMGApp import *
> >   File "/Library/Python/2.7/site-packages/pmg_tk/PMGApp.py", line 33, in
> > <module>
> >     class PMGApp(Pmw.MegaWidget):
> >   File
> > "/Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwLoader.py", line
> > 131, in __getattr__
> >     self._initialise()
> >   File
> > "/Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwLoader.py", line
> > 89, in _initialise
> >     raise ImportError(msg)
> >
> > This is preventing it from opening the GUI. Do you have any idea what
> > should I do to avoid this.
> >
> > Thanks for your help.
> >
> > Rhitankar
> >
> >
> > On Sat, May 4, 2013 at 6:21 AM, Thomas Holder wrote:
> >
> >     Hi Rhitankar,
> >
> >     looks like you installed the python3 version of Pmw which is not
> >     compatible with python 2.7.
> >
> >     Cheers,
> >       Thomas
> >
> >     Rhitankar Pal wrote, On 05/03/13 21:16:
> >     > Dear Pymol developers,
> >     >
> >     > I have recently installed pymol 1.6.x in MAC OS X 10.8.2 and have
> the
> >     > following error while opening the GUI
> >     >
> >     > Traceback (most recent call last):
> >     >   File "/Library/Python/2.7/site-packages/pmg_tk/__init__.py",
> >     line 35,
> >     > in run
> >     >     PMGApp(pymol_instance,skin).run(poll)
> >     >   File "/Library/Python/2.7/site-packages/pmg_tk/PMGApp.py", line
> 325,
> >     > in __init__
> >     >     self.runSkin()
> >     >   File "/Library/Python/2.7/site-packages/pmg_tk/PMGApp.py", line
> 251,
> >     > in runSkin
> >     >     self.skin.setup()
> >     >   File
> >     >
> "/Library/Python/2.7/site-packages/pmg_tk/skins/normal/__init__.py",
> >     > line 3661, in setup
> >     >     self.createInterface()
> >     >   File
> >     >
> "/Library/Python/2.7/site-packages/pmg_tk/skins/normal/__init__.py",
> >     > line 3634, in createInterface
> >     >     self.balloon = Pmw.Balloon(self.root)
> >     >   File
> >     >
> "/Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwBalloon.py",
> >     > line 28, in __init__
> >     >     Pmw.MegaToplevel.__init__(self, parent)
> >     >   File
> >     "/Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwBase.py",
> >     > line 982, in __init__
> >     >     super().__init__(parent, tkinter.Toplevel)
> >     > TypeError: super() takes at least 1 argument (0 given)
> >     >
> >     > As a result it never opens the "The Pymol Molecular Graphics
> System"
> >     > window. Can anyone help to find out what might be wrong.
> >     >
> >     > Thanks
> >     > Rhitankar
> > --
> > Rhitankar Pal
> > Postdoctoral Researcher,
> > Dept of Chemistry, Yale University
> > New Haven, CT 06511
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
>
>
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-- 
Rhitankar Pal
Postdoctoral Researcher,
Dept of Chemistry, Yale University
New Haven, CT 06511