Re: Issue with Pymol/CCPN menus after Relax install -- March 19, 2015 - 19:58

Hi Edward,

Thank you for the quick reply. Here's a rundown of the things I've tried
and what ended up working. I'm not sure what caused the problem -- I don't
think it was Relax. In the end I uninstalled everything from macports and
tried to just install pymol from macports:

sudo port uninstall installed

sudo port install pymol

This did not work, same tk issue (no menu). Then I read some forum post
that suggested an install of tcl no corefounation and tk no quartz before
pymol.

sudo port install tcl -corefoundation
sudo port install tk -quartz
sudo port install pymol

This worked! tk menus for Pymol and CCPN work fine.

Now, to see if Relax was the problem. I install Relax with MacPorts:

sudo port install relax

relax

I get the following output on the terminal:

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/wx-3.0-osx_cocoa/wx/_core.py:16633:
UserWarning: wxPython/wxWidgets release number mismatch
  warnings.warn("wxPython/wxWidgets release number mismatch")



                                            relax 3.3.6

                              Molecular dynamics by NMR data analysis

                             Copyright (C) 2001-2006 Edward d'Auvergne
                         Copyright (C) 2006-2015 the relax development team

This is free software which you are welcome to modify and redistribute
under the conditions of the
GNU General Public License (GPL).  This program, including all
modules, is licensed under the GPL
and comes with absolutely no warranty.  For details type 'GPL' within
the relax prompt.

Assistance in using the relax prompt and scripting interface can be
accessed by typing 'help' within
the prompt.

Processor fabric:  Uni-processor.

[94mrelax> [0m



No GUI, but I'm unsure if the MacPorts version should be with GUI.

But...pymol/ccpn are still work fine.

Finally, I installed relax-3.3.7.Darwin.dmg, reboot (just in case), still
everything seems fine and relax.app opens with the GUI and Pymol/CCPN are
also fine.

Thanks again for your quick responses Edward.

Best Regards,
Lisa




On Thu, Mar 19, 2015 at 11:09 AM, Edward d'Auvergne <edward@xxxxxxxxxxxxx>
wrote:

> Hi Lisa,
>
> Welcome to the relax mailing lists!  I think Jack might be able to
> answer this better, as he appears to be in charge of these packages at
> MacPorts:
>
> https://www.macports.org/ports.php?by=name&substr=relax
> https://www.macports.org/ports.php?by=name&substr=pymol
> https://www.macports.org/ports.php?by=name&substr=CCPN
>
> When you installed relax for the first time from MacPorts, was there
> any other software installed at around the same time?  Especially
> non-MacPorts libraries.  For installing relax the second time, did you
> use the DMG file at http://www.nmr-relax.com/download.html#Mac_OS_X ?
> If so, this is fully independent and shouldn't touch any parts of the
> system - all dependencies are built into it.  The problems you see
> cannot be due to relax itself, but maybe you could try uninstalling
> the MacPorts versions of relax, PyMOL, CCPN and importantly all their
> dependencies (py27-numpy py27-scipy py27-wxpython-3.0 pymol python27
> scons for relax) and then try to reinstall PyMOL and CCPN.  Maybe it
> is the dependencies that are the issue.  Maybe py27-wxpython-3.0
> clashes with py27-tkinter, though that is extremely unlikely.  If it
> is a tk problem, which I have seen before, then the entire PyMOL tk
> window will refuse to start and you'll only have the OpenGL window and
> an error message about the tk problem.  It is a very strange problem,
> and maybe Jack has better insight as to what is happening.
>
> Regards,
>
> Edward
>
>
>
> On 19 March 2015 at 17:44, Lisa Warner <lisa.warner@xxxxxxxxx> wrote:
> > Hi All,
> >
> > I'm not sure if this is a forum topic or not. Recently all of the menu
> > graphics for pymol and ccpn analysis stopped working shortly after I
> > installed Relax, which is why I'm posting this. Initially, I installed
> the
> > Macports version of Relax, but then noticed that it wasn't as up-to-date
> as
> > the current distribution on the Stand-Alone distribution on the Relax
> > website, so I installed that. It was a short time after that I noticed
> that
> > pymol/analysis menus were not working anymore. The problem could be
> > anything at this point, maybe not Relax related at all. I'm just trying
> to
> > figure things out. I think this is a tk-related issue. (I have already
> > tried to reinstall with the -no_tkinter suggestion).
> >
> > My question is this:
> >
> > Do the python packages that go with the stand-alone Relax get put into or
> > overwrite the system files? /usr/bin/?
> >
> > Even if they do, it shouldn't matter because all of my dependencies for
> > Pymol/CCPN should be sourcing the macports install dir /opt/local/bin...
> >
> > I've uninstalled all Relax and all softwares installed with Macports and
> > reinstalled only pymol and it's dependencies to try to tease out the
> > problem. But even after removing everything and a fresh install of
> Pymol, I
> > still have the same problem.
> >
> > I realize this may not even be a problem from Relax, but if you have any
> > advice, I'd greatly appreciate it.
> >
> > Thanks --
> > Lisa
> > _______________________________________________
> > relax (http://www.nmr-relax.com)
> >
> > This is the relax-users mailing list
> > relax-users@xxxxxxx
> >
> > To unsubscribe from this list, get a password
> > reminder, or change your subscription options,
> > visit the list information page at
> > https://mail.gna.org/listinfo/relax-users