Re: [PyMOL] Pymol Command window not displaying

[Julian Heinrich]

Hi,

are you trying to run PyMOL remotely, i.e. via ssh from your cluster?
This might work if you forward X11 to your local machine, though I'm not
sure if it supports OpenGL.

Looking at the error message, another possibility might be a missing tcl/tk
library?

Good luck,
Julian

On Tue, Sep 20, 2016 at 7:24 AM Srikanth Gumma 
wrote:

> Hi,
>
> Can anyone help me on this regard.
>
> Thanks
>
> -Srikanth.
>
> On Thu, Sep 1, 2016 at 10:19 PM, Thomas Holder <
> thomas.hol...@schrodinger.com> wrote:
>
>> Hi Srikanth,
>>
>> Is your custom Python installation properly set up with the custom Tcl/Tk
>> installation? Does the following work and open a Tk window?
>>
>> shell> /app/python/intel/2.7.12/bin/python # path guessed
>> python> import Tkinter
>> python> Tkinter.Tk()
>>
>> If not, then I think you need to set TCL_LIBRARY and/or TK_LIBRARY
>> environment variables first.
>>
>> Hope that helps.
>>
>> Cheers,
>>   Thomas
>>
>> On 31 Aug 2016, at 00:46, Srikanth Gumma  wrote:
>>
>> > Hi,
>> >
>> > I recently installed pymol from source using python-2.7.12 in my
>> cluster. I have to install python, tcl in a non standard location as this
>> is a cluster.
>> >
>> > After successful installation of pymol, I'm facing an issue while
>> opening pymol. I'm not able to see pymol command window, and receiving the
>> below error on the console.
>> >
>> > PyMOL(TM) Molecular Graphics System, Version 1.8.2.0.
>> >  Copyright (c) Schrodinger, LLC.
>> >  All Rights Reserved.
>> >
>> > Created by Warren L. DeLano, Ph.D.
>> >
>> > PyMOL is user-supported open-source software.  Although some
>> versions
>> > are freely available, PyMOL is not in the public domain.
>> >
>> > If PyMOL is helpful in your work or study, then please volunteer
>> > support for our ongoing efforts to create open and affordable
>> scientific
>> > software by purchasing a PyMOL Maintenance and/or Support
>> subscription.
>> >
>> > More information can be found at "http://www.pymol.org;.
>> >
>> > Enter "help" for a list of commands.
>> > Enter "help " for information on a specific command.
>> >
>> >  Hit ESC anytime to toggle between text and graphics.
>> >
>> >  Detected OpenGL version prior to 2.0. Shaders and volumes unavailable.
>> >  OpenGL graphics engine:
>> >   GL_VENDOR:   Intel
>> >   GL_RENDERER: Intel(R) HD Graphics 4600
>> >   GL_VERSION:  1.4 (4.0.0 - Build 9.18.10.3272)
>> > Traceback (most recent call last):
>> >   File "/app/python/intel/pymol/lib/python/pmg_tk/__init__.py", line
>> 35, in run
>> > PMGApp(pymol_instance,skin).run(poll)
>> >   File "/app/python/intel/pymol/lib/python/pmg_tk/PMGApp.py", line 323,
>> in __init__
>> > self.root = Tk() # creates the root window for the application
>> >   File "/app/python/intel/2.7.12/lib/python2.7/lib-tk/Tkinter.py", line
>> 1815, in __init__
>> > self.tk = _tkinter.create(screenName, baseName, className,
>> interactive, wantobjects, useTk, sync, use)
>> > TclError: invalid command name "tcl_findLibrary"
>> >  Detected 24 CPU cores.  Enabled multithreaded rendering.
>> >
>> >
>> > Appreciate any help to resolve the issue.
>> >
>> > -srikanth
>>
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>>
>>
>
> --
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Re: [PyMOL] Pymol Command window not displaying

[Srikanth Gumma]

Hi,

Can anyone help me on this regard.

Thanks

-Srikanth.

On Thu, Sep 1, 2016 at 10:19 PM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:

> Hi Srikanth,
>
> Is your custom Python installation properly set up with the custom Tcl/Tk
> installation? Does the following work and open a Tk window?
>
> shell> /app/python/intel/2.7.12/bin/python # path guessed
> python> import Tkinter
> python> Tkinter.Tk()
>
> If not, then I think you need to set TCL_LIBRARY and/or TK_LIBRARY
> environment variables first.
>
> Hope that helps.
>
> Cheers,
>   Thomas
>
> On 31 Aug 2016, at 00:46, Srikanth Gumma  wrote:
>
> > Hi,
> >
> > I recently installed pymol from source using python-2.7.12 in my
> cluster. I have to install python, tcl in a non standard location as this
> is a cluster.
> >
> > After successful installation of pymol, I'm facing an issue while
> opening pymol. I'm not able to see pymol command window, and receiving the
> below error on the console.
> >
> > PyMOL(TM) Molecular Graphics System, Version 1.8.2.0.
> >  Copyright (c) Schrodinger, LLC.
> >  All Rights Reserved.
> >
> > Created by Warren L. DeLano, Ph.D.
> >
> > PyMOL is user-supported open-source software.  Although some versions
> > are freely available, PyMOL is not in the public domain.
> >
> > If PyMOL is helpful in your work or study, then please volunteer
> > support for our ongoing efforts to create open and affordable
> scientific
> > software by purchasing a PyMOL Maintenance and/or Support
> subscription.
> >
> > More information can be found at "http://www.pymol.org;.
> >
> > Enter "help" for a list of commands.
> > Enter "help " for information on a specific command.
> >
> >  Hit ESC anytime to toggle between text and graphics.
> >
> >  Detected OpenGL version prior to 2.0. Shaders and volumes unavailable.
> >  OpenGL graphics engine:
> >   GL_VENDOR:   Intel
> >   GL_RENDERER: Intel(R) HD Graphics 4600
> >   GL_VERSION:  1.4 (4.0.0 - Build 9.18.10.3272)
> > Traceback (most recent call last):
> >   File "/app/python/intel/pymol/lib/python/pmg_tk/__init__.py", line
> 35, in run
> > PMGApp(pymol_instance,skin).run(poll)
> >   File "/app/python/intel/pymol/lib/python/pmg_tk/PMGApp.py", line 323,
> in __init__
> > self.root = Tk() # creates the root window for the application
> >   File "/app/python/intel/2.7.12/lib/python2.7/lib-tk/Tkinter.py", line
> 1815, in __init__
> > self.tk = _tkinter.create(screenName, baseName, className,
> interactive, wantobjects, useTk, sync, use)
> > TclError: invalid command name "tcl_findLibrary"
> >  Detected 24 CPU cores.  Enabled multithreaded rendering.
> >
> >
> > Appreciate any help to resolve the issue.
> >
> > -srikanth
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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Re: [PyMOL] Pymol Command window not displaying

[Thomas Holder]

Hi Srikanth,

Is your custom Python installation properly set up with the custom Tcl/Tk 
installation? Does the following work and open a Tk window?

shell> /app/python/intel/2.7.12/bin/python # path guessed
python> import Tkinter
python> Tkinter.Tk()

If not, then I think you need to set TCL_LIBRARY and/or TK_LIBRARY environment 
variables first.

Hope that helps.

Cheers,
  Thomas

On 31 Aug 2016, at 00:46, Srikanth Gumma  wrote:

> Hi,
> 
> I recently installed pymol from source using python-2.7.12 in my cluster. I 
> have to install python, tcl in a non standard location as this is a cluster. 
> 
> After successful installation of pymol, I'm facing an issue while opening 
> pymol. I'm not able to see pymol command window, and receiving the below 
> error on the console. 
> 
> PyMOL(TM) Molecular Graphics System, Version 1.8.2.0.
>  Copyright (c) Schrodinger, LLC.
>  All Rights Reserved.
> 
> Created by Warren L. DeLano, Ph.D.
> 
> PyMOL is user-supported open-source software.  Although some versions
> are freely available, PyMOL is not in the public domain.
> 
> If PyMOL is helpful in your work or study, then please volunteer
> support for our ongoing efforts to create open and affordable scientific
> software by purchasing a PyMOL Maintenance and/or Support subscription.
> 
> More information can be found at "http://www.pymol.org;.
> 
> Enter "help" for a list of commands.
> Enter "help " for information on a specific command.
> 
>  Hit ESC anytime to toggle between text and graphics.
> 
>  Detected OpenGL version prior to 2.0. Shaders and volumes unavailable.
>  OpenGL graphics engine:
>   GL_VENDOR:   Intel
>   GL_RENDERER: Intel(R) HD Graphics 4600
>   GL_VERSION:  1.4 (4.0.0 - Build 9.18.10.3272)
> Traceback (most recent call last):
>   File "/app/python/intel/pymol/lib/python/pmg_tk/__init__.py", line 35, in 
> run
> PMGApp(pymol_instance,skin).run(poll)
>   File "/app/python/intel/pymol/lib/python/pmg_tk/PMGApp.py", line 323, in 
> __init__
> self.root = Tk() # creates the root window for the application
>   File "/app/python/intel/2.7.12/lib/python2.7/lib-tk/Tkinter.py", line 1815, 
> in __init__
> self.tk = _tkinter.create(screenName, baseName, className, interactive, 
> wantobjects, useTk, sync, use)
> TclError: invalid command name "tcl_findLibrary"
>  Detected 24 CPU cores.  Enabled multithreaded rendering.
> 
> 
> Appreciate any help to resolve the issue. 
> 
> -srikanth

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] Pymol Command window not displaying

[Srikanth Gumma]

Hi,

I recently installed pymol from source using python-2.7.12 in my cluster. I
have to install python, tcl in a non standard location as this is a
cluster.

After successful installation of pymol, I'm facing an issue while opening
pymol. I'm not able to see pymol command window, and receiving the below
error on the console.

PyMOL(TM) Molecular Graphics System, Version 1.8.2.0.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.

Created by Warren L. DeLano, Ph.D.

PyMOL is user-supported open-source software.  Although some versions
are freely available, PyMOL is not in the public domain.

If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.

More information can be found at "http://www.pymol.org;.

Enter "help" for a list of commands.
Enter "help " for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Detected OpenGL version prior to 2.0. Shaders and volumes unavailable.
 OpenGL graphics engine:
  GL_VENDOR:   Intel
  GL_RENDERER: Intel(R) HD Graphics 4600
  GL_VERSION:  1.4 (4.0.0 - Build 9.18.10.3272)
Traceback (most recent call last):
  File "/app/python/intel/pymol/lib/python/pmg_tk/__init__.py", line 35, in
run
PMGApp(pymol_instance,skin).run(poll)
  File "/app/python/intel/pymol/lib/python/pmg_tk/PMGApp.py", line 323, in
__init__
self.root = Tk() # creates the root window for the application
  File "/app/python/intel/2.7.12/lib/python2.7/lib-tk/Tkinter.py", line
1815, in __init__
self.tk = _tkinter.create(screenName, baseName, className, interactive,
wantobjects, useTk, sync, use)
TclError: invalid command name "tcl_findLibrary"
 Detected 24 CPU cores.  Enabled multithreaded rendering.


Appreciate any help to resolve the issue.

-srikanth
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