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From: Rhitankar P. <rhi...@gm...> - 2013-05-03 19:16:29
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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
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From: Thomas H. <tho...@sc...> - 2013-05-04 10:21:40
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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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From: Rhitankar P. <rhi...@gm...> - 2013-05-07 00:20:32
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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 <tho...@sc... > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 |
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From: Rhitankar P. <rhi...@gm...> - 2013-05-07 00:27:05
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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 <rhi...@gm...> 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 < > tho...@sc...> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > 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 |
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From: David H. <li...@co...> - 2013-05-07 16:30:40
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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 <rhi...@gm...> 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 <rhi...@gm...> 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 < >> tho...@sc...> 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 (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >>> >> >> >> >> -- >> 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
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From: Rhitankar P. <rhi...@gm...> - 2013-05-07 17:32:34
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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...@co...> 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 <rhi...@gm...> 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 <rhi...@gm...>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 < >>> tho...@sc...> 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 (PyM...@li...) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pym...@li... >>>> >>> >>> >>> >>> -- >>> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 |
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From: David H. <li...@co...> - 2013-05-07 21:28:50
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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 <rhi...@gm...> 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...@co...> 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 <rhi...@gm...>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 <rhi...@gm...>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 < >>>> tho...@sc...> 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 (PyM...@li...) >>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>> Archives: >>>>> http://www.mail-archive.com/pym...@li... >>>>> >>>> >>>> >>>> >>>> -- >>>> 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 (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >>> >> >> > > > -- > Rhitankar Pal > Postdoctoral Researcher, > Dept of Chemistry, Yale University > New Haven, CT 06511 > |
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From: Bishwa S. <bp...@ut...> - 2013-05-08 11:48:25
|
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 bs...@bt...<mailto:bs...@bt...> |
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From: Thomas H. <tho...@sc...> - 2013-05-08 14:33:54
|
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 |
|
From: Rhitankar P. <rhi...@gm...> - 2013-05-08 16:01:50
|
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 <tho...@sc...
> 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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> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
--
Rhitankar Pal
Postdoctoral Researcher,
Dept of Chemistry, Yale University
New Haven, CT 06511
|
|
From: Thomas H. <tho...@sc...> - 2013-05-08 16:34:28
|
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 |
|
From: Rhitankar P. <rhi...@gm...> - 2013-05-08 16:46:27
|
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 > > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 |
|
From: Thomas H. <tho...@sc...> - 2013-05-08 21:32:16
|
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 |
|
From: Thomas H. <tho...@sc...> - 2013-05-08 21:44:04
|
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 |
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