Re: [PyMOL] Secondary structure labeling
Hi All, I am using Pymol to make figures for my publication. I am not sure if there has been a discussion earlier but I would like to know how we can label the secondary structures (helices and strands) using Pymol. I have them defined in my header file using DSSP. Thank you in advance. Bishwa Subedi bsub...@btk.fimailto:bsub...@btk.fi -- 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] Secondary structure labeling
Hi Bishwa, can you be more precise what you mean by label? If the secondary structure is defined in the header of your PDB file, PyMOL can show cartoon representation, show text labels on C-alpha atoms and color by secondary structure. PyMOL as cartoon PyMOL label name CA, ss PyMOL color red, ss H PyMOL color yellow, ss S Cheers, Thomas Bishwa Subedi wrote, On 05/08/13 13:33: Hi All, I am using Pymol to make figures for my publication. I am not sure if there has been a discussion earlier but I would like to know how we can label the secondary structures (helices and strands) using Pymol. I have them defined in my header file using DSSP. Thank you in advance. Bishwa Subedi -- 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, 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] Secondary structure labeling
Hi Bishwa, what you want is to label one representative atom per secondary structure element. So figure out chain and residue number of those atoms, and label each of them individually: PyMOL label A/42/CA, beta1 PyMOL label A/117/CA, alpha1 PyMOL label A/147/CA, alpha2 For changing label font, size, color etc., see: http://pymolwiki.org/index.php/Label Cheers, Thomas Bishwa Subedi wrote, On 05/08/13 21:50: Dear Thomas, Thank you. The one you said is to show molecule as cartoon and color according to the secondary structure. But I would like to label/name the alpha helices as alpha1...and beta strands as Beta1 and so on. Can that be done using Pymol. Best Bishwa Subedi, M.Sc Bioinformatics University of Turku Finland On May 8, 2013, at 5:33 PM, Thomas Holder wrote: Hi Bishwa, can you be more precise what you mean by label? If the secondary structure is defined in the header of your PDB file, PyMOL can show cartoon representation, show text labels on C-alpha atoms and color by secondary structure. PyMOL as cartoon PyMOL label name CA, ss PyMOL color red, ss H PyMOL color yellow, ss S Cheers, Thomas Bishwa Subedi wrote, On 05/08/13 13:33: Hi All, I am using Pymol to make figures for my publication. I am not sure if there has been a discussion earlier but I would like to know how we can label the secondary structures (helices and strands) using Pymol. I have them defined in my header file using DSSP. Thank you in advance. Bishwa Subedi -- 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
