Re: [PyMOL] Pymol error
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 thomas.hol...@schrodinger.com 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 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol error
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 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol error
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 thomas.hol...@schrodinger.com 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 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This
Re: [PyMOL] Pymol error
Hi Rhitankar, this depends which python you used and which arguments you passed to setup.py. I assume you used system python and no arguments, then just remove these: /Library/Python/2.7/site-packages/pymol /usr/local/bin/pymol Cheers, Thomas Rhitankar Pal wrote, On 05/08/13 18:46: 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 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 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed
Re: [PyMOL] Pymol error
by default, macports installs tcl with the +corefoundation variant (see http://guide.macports.org/#using.variants ) if you do: sudo port install tcl -corefoundation that will solve the problem. -David On Mon, May 6, 2013 at 8:26 PM, Rhitankar Pal rhitan...@gmail.com wrote: Dear Thomas, One more question. When I tried to install pymol using port [ sudo port install pymol ] I get the following error message: Error: org.macports.archivefetch for port pymol returned: tcl must be installed without +corefoundation. Do you have any idea why there is this error message? Eventually I downloaded the tar.gz and installed it using the setup.py inside. Which is apparently not compatible with the Pmw2 and therefore gave the error I mentioned in my previous email. Any help would be appreciated Thanks Rhitankar On Mon, May 6, 2013 at 8:20 PM, Rhitankar Pal rhitan...@gmail.com wrote: Dear Thomas, Now I have installed Pmw.1.3 which should be the one compatible with python2.7 I guess. However I am still getting the same error. I think pymol is trying to use Pmw2 by default. Is there any way we can ask it to use 1.3 instead? Thanks for your help Rhitankar On Sat, May 4, 2013 at 6:21 AM, Thomas Holder thomas.hol...@schrodinger.com 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 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page:
Re: [PyMOL] Pymol error
Hi David, I installed tcl without the corefoundation and now while trying to install pymol I am getting the following error message: Error: org.macports.archivefetch for port pymol returned: tk must be installed without +quartz. How can I install tk without +quartz? Are these issues happening because OSX 10.8.2 comes with preinstalled tcl and tk ? Thanks Rhitankar On Tue, May 7, 2013 at 12:30 PM, David Hall li...@cowsandmilk.net wrote: by default, macports installs tcl with the +corefoundation variant (see http://guide.macports.org/#using.variants ) if you do: sudo port install tcl -corefoundation that will solve the problem. -David On Mon, May 6, 2013 at 8:26 PM, Rhitankar Pal rhitan...@gmail.com wrote: Dear Thomas, One more question. When I tried to install pymol using port [ sudo port install pymol ] I get the following error message: Error: org.macports.archivefetch for port pymol returned: tcl must be installed without +corefoundation. Do you have any idea why there is this error message? Eventually I downloaded the tar.gz and installed it using the setup.py inside. Which is apparently not compatible with the Pmw2 and therefore gave the error I mentioned in my previous email. Any help would be appreciated Thanks Rhitankar On Mon, May 6, 2013 at 8:20 PM, Rhitankar Pal rhitan...@gmail.comwrote: Dear Thomas, Now I have installed Pmw.1.3 which should be the one compatible with python2.7 I guess. However I am still getting the same error. I think pymol is trying to use Pmw2 by default. Is there any way we can ask it to use 1.3 instead? Thanks for your help Rhitankar On Sat, May 4, 2013 at 6:21 AM, Thomas Holder thomas.hol...@schrodinger.com 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 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511
Re: [PyMOL] Pymol error
sudo port install tk -quartz It has nothing to do with what OS X ships with, it has to do with current macports defaults, which changed around 18 months ago. You can dig around the macports bug reports to see discussion of the change. -David On Tue, May 7, 2013 at 1:32 PM, Rhitankar Pal rhitan...@gmail.com wrote: Hi David, I installed tcl without the corefoundation and now while trying to install pymol I am getting the following error message: Error: org.macports.archivefetch for port pymol returned: tk must be installed without +quartz. How can I install tk without +quartz? Are these issues happening because OSX 10.8.2 comes with preinstalled tcl and tk ? Thanks Rhitankar On Tue, May 7, 2013 at 12:30 PM, David Hall li...@cowsandmilk.net wrote: by default, macports installs tcl with the +corefoundation variant (see http://guide.macports.org/#using.variants ) if you do: sudo port install tcl -corefoundation that will solve the problem. -David On Mon, May 6, 2013 at 8:26 PM, Rhitankar Pal rhitan...@gmail.comwrote: Dear Thomas, One more question. When I tried to install pymol using port [ sudo port install pymol ] I get the following error message: Error: org.macports.archivefetch for port pymol returned: tcl must be installed without +corefoundation. Do you have any idea why there is this error message? Eventually I downloaded the tar.gz and installed it using the setup.py inside. Which is apparently not compatible with the Pmw2 and therefore gave the error I mentioned in my previous email. Any help would be appreciated Thanks Rhitankar On Mon, May 6, 2013 at 8:20 PM, Rhitankar Pal rhitan...@gmail.comwrote: Dear Thomas, Now I have installed Pmw.1.3 which should be the one compatible with python2.7 I guess. However I am still getting the same error. I think pymol is trying to use Pmw2 by default. Is there any way we can ask it to use 1.3 instead? Thanks for your help Rhitankar On Sat, May 4, 2013 at 6:21 AM, Thomas Holder thomas.hol...@schrodinger.com 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 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may
Re: [PyMOL] Pymol error
Dear Thomas, Now I have installed Pmw.1.3 which should be the one compatible with python2.7 I guess. However I am still getting the same error. I think pymol is trying to use Pmw2 by default. Is there any way we can ask it to use 1.3 instead? Thanks for your help Rhitankar On Sat, May 4, 2013 at 6:21 AM, Thomas Holder thomas.hol...@schrodinger.com 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 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol error
Dear Thomas, One more question. When I tried to install pymol using port [ sudo port install pymol ] I get the following error message: Error: org.macports.archivefetch for port pymol returned: tcl must be installed without +corefoundation. Do you have any idea why there is this error message? Eventually I downloaded the tar.gz and installed it using the setup.py inside. Which is apparently not compatible with the Pmw2 and therefore gave the error I mentioned in my previous email. Any help would be appreciated Thanks Rhitankar On Mon, May 6, 2013 at 8:20 PM, Rhitankar Pal rhitan...@gmail.com wrote: Dear Thomas, Now I have installed Pmw.1.3 which should be the one compatible with python2.7 I guess. However I am still getting the same error. I think pymol is trying to use Pmw2 by default. Is there any way we can ask it to use 1.3 instead? Thanks for your help Rhitankar On Sat, May 4, 2013 at 6:21 AM, Thomas Holder thomas.hol...@schrodinger.com 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 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol error
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 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Pymol error
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 -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Pymol error in Mac OS X 10.8.2
I am having some issues after installing pymol in Mac OS 10.8.2. It seems the program is installed but when I try to open in using command line pymol it doesn't show the 'Molecular Graphics System' window but shows only the 'Pymol Viewer' window. In the terminal I have the following error message: Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.20. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: NVIDIA GeForce GT 640M OpenGL Engine GL_VERSION: 2.1 NVIDIA-8.10.44 304.10.65f03 Traceback (most recent call last): 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, - Ignored: 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) ImportError: No module named tkinter Detected 4 CPU cores. Enabled multithreaded rendering. Any help to resolve this issue would be greatly appreciated. Thanks Rhitankar -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol error in Mac OS X 10.8.2
what method did you use for installation? -- David Hall On Wednesday, May 1, 2013 at 11:53 AM, Rhitankar Pal wrote: I am having some issues after installing pymol in Mac OS 10.8.2. It seems the program is installed but when I try to open in using command line pymol it doesn't show the 'Molecular Graphics System' window but shows only the 'Pymol Viewer' window. In the terminal I have the following error message: Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.20. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: NVIDIA GeForce GT 640M OpenGL Engine GL_VERSION: 2.1 NVIDIA-8.10.44 304.10.65f03 Traceback (most recent call last): 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, - Ignored: 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) ImportError: No module named tkinter Detected 4 CPU cores. Enabled multithreaded rendering. Any help to resolve this issue would be greatly appreciated. Thanks Rhitankar -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net (mailto:PyMOL-users@lists.sourceforge.net)) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] pymol error for all pdb files
Dear Pymol users, I installed Pymol 1.2 on Ubuntu 9.1 but I have the error as the following for all PDB files. (Select File - open from the user menu, and select and open that PDB file). *Error: 1* *type 'exceptions.UnicodeEncodeError' Exception in Tk callback* * Function: bound method Normal.file_open of pmg_tk.skins.normal.Normal instance at 0x9f3270c (type: type 'instancemethod')* * Args: ()* *Traceback (innermost last):* * File /usr/lib/python2.6/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line 1747, in __call__* *return apply(self.func, args)* * File /usr/lib/pymodules/python2.6/pmg_tk/skins/normal/__init__.py, line 544, in file_open* *self.cmd.load(ofile,quiet=0)* * File /usr/lib/pymodules/python2.6/pymol/importing.py, line 869, in load* *_self.unlock(r,_self)* * File /usr/lib/pymodules/python2.6/pymol/locking.py, line 99, in unlock* *_self.lock_api.release()* * File /usr/lib/python2.6/threading.py, line 135, in release* *if self.__owner is not current_thread():* * File /usr/lib/python2.6/threading.py, line 803, in currentThread* *return _active[_get_ident()]* *type 'exceptions.UnicodeEncodeError': 'ascii' codec can't encode character u'\xfc' in position 13: ordinal not in range(128)* What should I do? Thanks in advance -- Ahmet YILDIRIM -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] [PYMOL] error with pair fitting
Hi Jorgen, I just tried pair fitting some atoms from your PyMOL session and was able to reproduce what you found. Pair fitting is done between atoms, so please show lines or sticks, not just cartoons, when pair fitting. You can turn off the lines later if you don't need them. In this way, you can select just one atom at a time and PyMOL will be happy. The error begins when one selects an entire residue for pair fitting; PyMOL doesn't know how to pair fit an entire residue--though, maybe it should. If you choose a single atom, sometimes PyMOL will output, Selector: selection sele defined with 1 atoms. sele and not _pf_s_* but this should not break the fitting of the Pair Fitting wizard. If the error occurs, please either click Clear in the wizard or restart the Pair Fitting wizard altogether, while ensuring that you select just one atom a time. Cheers, -- Jason On Tue, Oct 5, 2010 at 8:58 AM, Jorgen Ravoet jorgen.rav...@gmail.com wrote: Hello, I have loaded two PDB files in PyMol to pair fit some of their amino acids. When using the wizard, I'm getiing the following error. Does anyone has an idea how to solve this? _seeker and not _pf_s_* Editor-Error: Invalid input. Traceback (most recent call last): File C:\Program Files (x86)\DeLano Scientific\PyMOL/modules\pymol\wizard\pair_fit.py, line 147, in do_select cmd.edit(name + and not + sele_prefix + *) # note, using new object name wildcards File C:\Program Files (x86)\DeLano Scientific\PyMOL/modules\pymol\editing.py, line 851, in edit if _self._raising(r,_self): raise pymol.CmdException CmdException: pymol.CmdException instance at 0x0379D378 Jorgen Ravoet Molecular biologist -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] [PYMOL] error with pair fitting
Hello, I have loaded two PDB files in PyMol to pair fit some of their amino acids. When using the wizard, I'm getiing the following error. Does anyone has an idea how to solve this? _seeker and not _pf_s_* Editor-Error: Invalid input. Traceback (most recent call last): File C:\Program Files (x86)\DeLano Scientific\PyMOL/modules\pymol\wizard\pair_fit.py, line 147, in do_select cmd.edit(name + and not + sele_prefix + *) # note, using new object name wildcards File C:\Program Files (x86)\DeLano Scientific\PyMOL/modules\pymol\editing.py, line 851, in edit if _self._raising(r,_self): raise pymol.CmdException CmdException: pymol.CmdException instance at 0x0379D378 Jorgen Ravoet Molecular biologist -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] [PYMOL] error with pair fitting
Hi Jorgen, I cannot reproduce this. Can you please give me the PDBs (or PDB IDs) and commands to reproduce this error? Thanks, -- Jason On Tue, Oct 5, 2010 at 8:58 AM, Jorgen Ravoet jorgen.rav...@gmail.com wrote: Hello, I have loaded two PDB files in PyMol to pair fit some of their amino acids. When using the wizard, I'm getiing the following error. Does anyone has an idea how to solve this? _seeker and not _pf_s_* Editor-Error: Invalid input. Traceback (most recent call last): File C:\Program Files (x86)\DeLano Scientific\PyMOL/modules\pymol\wizard\pair_fit.py, line 147, in do_select cmd.edit(name + and not + sele_prefix + *) # note, using new object name wildcards File C:\Program Files (x86)\DeLano Scientific\PyMOL/modules\pymol\editing.py, line 851, in edit if _self._raising(r,_self): raise pymol.CmdException CmdException: pymol.CmdException instance at 0x0379D378 Jorgen Ravoet Molecular biologist -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] pymol error in linux - does not work
Praba, You need to install 32-bit compatibility libraries for X11, which should provide the file in /usr/lib or /usr/X11R6/lib Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of praba ponraj Sent: Friday, February 08, 2008 1:46 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] pymol error in linux - does not work Pymol users on Linux, I installed the Pymol (pymol-1_or2) on my new Red Hat Enterprise Linux Client release 5.1 (Tikanga). When I type the pymol after installing, I get the error pymol.exe: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory The file libXmu.so.6 is at /usr/lib64 Can anyone help? Thanks. Praba
