Discussion:
[PyMOL] plugin errors in pymol 1.7.2.1
Hena Dutta
2014-12-20 19:08:29 UTC
Permalink
Dear Pymol Users,
I installed pymol 1.7.2.1 in my laptop (windows 8.1) and found some errors.
Please see the highlighted portion below.

How can I see stereo, although it has been enabled?
I installed Openbabel, but some plug-in are not being initialized.
Could you please suggest how can I solve these problems?

Best regards,
Hena


After running the program I found some
PyMOL(TM) Molecular Graphics System, Version 1.7.2.1.
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 <command-name>" for information on a specific command.

Hit ESC anytime to toggle between text and graphics.

Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 4.40.
OpenGL graphics engine:
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: GeForce GTX 670M/PCIe/SSE2
GL_VERSION: 4.4.0 NVIDIA 344.60
Detected 8 CPU cores. Enabled multithreaded rendering.



OpenGL quad-buffer stereo 3D detected and enabled.
Executive: Loading version 1.600 session...
Unable to initialize plugin 'mtsslDockGui' (pmg_tk.startup.mtsslDockGui).
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

Optimize plug-in needs openbabel to be installed in your system, please
follow the instructions at
http://openbabel.org/wiki/Get_Open_Babel
Unable to initialize plugin 'mtsslWizard' (pmg_tk.startup.mtsslWizard).
Unable to initialize plugin 'mtsslTrilaterate'
(pmg_tk.startup.mtsslTrilaterate).
Osvaldo Martin
2014-12-20 21:12:37 UTC
Permalink
Hi Hena,

Regarding Optimize plugin. You need to install OpenBabel and OpenBabel
Python bindings (see instructions here
<http://openbabel.org/wiki/Get_Open_Babel>). As far as I know for Windows
there is not a 64 bit version of OpenBabel and hence if you want to use
openbabel and optimize plugin on a 64 bit Windows you have to instal the
32-bit version of Python and PyMOL.

Regards,
Osvaldo.
Post by Hena Dutta
Dear Pymol Users,
I installed pymol 1.7.2.1 in my laptop (windows 8.1) and found some
errors. Please see the highlighted portion below.
How can I see stereo, although it has been enabled?
I installed Openbabel, but some plug-in are not being initialized.
Could you please suggest how can I solve these problems?
Best regards,
Hena
After running the program I found some
PyMOL(TM) Molecular Graphics System, Version 1.7.2.1.
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 <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 4.40.
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: GeForce GTX 670M/PCIe/SSE2
GL_VERSION: 4.4.0 NVIDIA 344.60
Detected 8 CPU cores. Enabled multithreaded rendering.
OpenGL quad-buffer stereo 3D detected and enabled.
Executive: Loading version 1.600 session...
Unable to initialize plugin 'mtsslDockGui' (pmg_tk.startup.mtsslDockGui).
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Optimize plug-in needs openbabel to be installed in your system, please
follow the instructions at
http://openbabel.org/wiki/Get_Open_Babel
Unable to initialize plugin 'mtsslWizard' (pmg_tk.startup.mtsslWizard).
Unable to initialize plugin 'mtsslTrilaterate'
(pmg_tk.startup.mtsslTrilaterate).
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Christoph Gohlke
2014-12-20 23:14:56 UTC
Permalink
Try the 64 bit version of OpenBabel at
<http://www.lfd.uci.edu/~gohlke/pythonlibs/#openbabel>

Christoph
Post by Osvaldo Martin
Hi Hena,
Regarding Optimize plugin. You need to install OpenBabel and OpenBabel
Python bindings (see instructions here
<http://openbabel.org/wiki/Get_Open_Babel>). As far as I know for
Windows there is not a 64 bit version of OpenBabel and hence if you want
to use openbabel and optimize plugin on a 64 bit Windows you have to
instal the 32-bit version of Python and PyMOL.
Regards,
Osvaldo.
Dear Pymol Users,
I installed pymol 1.7.2.1 in my laptop (windows 8.1) and found some
errors. Please see the highlighted portion below.
How can I see stereo, although it has been enabled?
I installed Openbabel, but some plug-in are not being initialized.
Could you please suggest how can I solve these problems?
Best regards,
Hena
After running the program I found some
PyMOL(TM) Molecular Graphics System, Version 1.7.2.1.
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 <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 4.40.
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: GeForce GTX 670M/PCIe/SSE2
GL_VERSION: 4.4.0 NVIDIA 344.60
Detected 8 CPU cores. Enabled multithreaded rendering.
OpenGL quad-buffer stereo 3D detected and enabled.
Executive: Loading version 1.600 session...
Unable to initialize plugin 'mtsslDockGui'
(pmg_tk.startup.mtsslDockGui).
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Optimize plug-in needs openbabel to be installed in your system,
please follow the instructions at
http://openbabel.org/wiki/Get_Open_Babel
Unable to initialize plugin 'mtsslWizard' (pmg_tk.startup.mtsslWizard).
Unable to initialize plugin 'mtsslTrilaterate'
(pmg_tk.startup.mtsslTrilaterate).
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
PyMOL-users mailing list (PyMOL-***@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-***@lists.sourceforge.net
Osvaldo Martin
2014-12-20 23:32:56 UTC
Permalink
Hi Christoph,

I do not use Windows. I would be very thankful if you could check that the
optimize-plugin works with the 64 bit version of OpenBabel that you
mention. Could you please confirm that?

Thanks in advance.
Osvaldo.
Post by Christoph Gohlke
Try the 64 bit version of OpenBabel at
<http://www.lfd.uci.edu/~gohlke/pythonlibs/#openbabel>
Christoph
Post by Osvaldo Martin
Hi Hena,
Regarding Optimize plugin. You need to install OpenBabel and OpenBabel
Python bindings (see instructions here
<http://openbabel.org/wiki/Get_Open_Babel>). As far as I know for
Windows there is not a 64 bit version of OpenBabel and hence if you want
to use openbabel and optimize plugin on a 64 bit Windows you have to
instal the 32-bit version of Python and PyMOL.
Regards,
Osvaldo.
Dear Pymol Users,
I installed pymol 1.7.2.1 in my laptop (windows 8.1) and found some
errors. Please see the highlighted portion below.
How can I see stereo, although it has been enabled?
I installed Openbabel, but some plug-in are not being initialized.
Could you please suggest how can I solve these problems?
Best regards,
Hena
After running the program I found some
PyMOL(TM) Molecular Graphics System, Version 1.7.2.1.
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 <command-name>" for information on a specific
command.
Post by Osvaldo Martin
Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 4.40.
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: GeForce GTX 670M/PCIe/SSE2
GL_VERSION: 4.4.0 NVIDIA 344.60
Detected 8 CPU cores. Enabled multithreaded rendering.
OpenGL quad-buffer stereo 3D detected and enabled.
Executive: Loading version 1.600 session...
Unable to initialize plugin 'mtsslDockGui'
(pmg_tk.startup.mtsslDockGui).
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Post by Osvaldo Martin
Optimize plug-in needs openbabel to be installed in your system,
please follow the instructions at
http://openbabel.org/wiki/Get_Open_Babel
Unable to initialize plugin 'mtsslWizard'
(pmg_tk.startup.mtsslWizard).
Post by Osvaldo Martin
Unable to initialize plugin 'mtsslTrilaterate'
(pmg_tk.startup.mtsslTrilaterate).
------------------------------------------------------------------------------
Post by Osvaldo Martin
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and
Dashboards
Post by Osvaldo Martin
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations,
FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
Post by Osvaldo Martin
_______________________________________________
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
------------------------------------------------------------------------------
Post by Osvaldo Martin
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
Post by Osvaldo Martin
_______________________________________________
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Christoph Gohlke
2014-12-21 06:15:53 UTC
Permalink
The optimize plugin loads and seems to work, i.e. it runs and produces
some output that looks reasonable. Is there a proper test for the
plugin? I tried to compare results to pymol on Ubuntu 14.10 but that
version is unstable...

Christoph
Post by Osvaldo Martin
Hi Christoph,
I do not use Windows. I would be very thankful if you could check that
the optimize-plugin works with the 64 bit version of OpenBabel that you
mention. Could you please confirm that?
Thanks in advance.
Osvaldo.
Try the 64 bit version of OpenBabel at
<http://www.lfd.uci.edu/~gohlke/pythonlibs/#openbabel
<http://www.lfd.uci.edu/%7Egohlke/pythonlibs/#openbabel>>
Christoph
Post by Osvaldo Martin
Hi Hena,
Regarding Optimize plugin. You need to install OpenBabel and OpenBabel
Python bindings (see instructions here
<http://openbabel.org/wiki/Get_Open_Babel>). As far as I know for
Windows there is not a 64 bit version of OpenBabel and hence if you want
to use openbabel and optimize plugin on a 64 bit Windows you have to
instal the 32-bit version of Python and PyMOL.
Regards,
Osvaldo.
Dear Pymol Users,
I installed pymol 1.7.2.1 in my laptop (windows 8.1) and found some
errors. Please see the highlighted portion below.
How can I see stereo, although it has been enabled?
I installed Openbabel, but some plug-in are not being initialized.
Could you please suggest how can I solve these problems?
Best regards,
Hena
After running the program I found some
PyMOL(TM) Molecular Graphics System, Version 1.7.2.1.
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 <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 4.40.
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: GeForce GTX 670M/PCIe/SSE2
GL_VERSION: 4.4.0 NVIDIA 344.60
Detected 8 CPU cores. Enabled multithreaded rendering.
OpenGL quad-buffer stereo 3D detected and enabled.
Executive: Loading version 1.600 session...
Unable to initialize plugin 'mtsslDockGui'
(pmg_tk.startup.mtsslDockGui).
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Optimize plug-in needs openbabel to be installed in your system,
please follow the instructions at
http://openbabel.org/wiki/Get_Open_Babel
Unable to initialize plugin 'mtsslWizard' (pmg_tk.startup.mtsslWizard).
Unable to initialize plugin 'mtsslTrilaterate'
(pmg_tk.startup.mtsslTrilaterate).
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration &
more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
Info Page:https://lists.sourceforge.net/lists/listinfo/pymol-users
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
Info Page:https://lists.sourceforge.net/lists/listinfo/pymol-users
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
PyMOL-users mailing list (PyMOL-***@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-***@lists.sourceforge.net
Thomas Holder
2014-12-22 15:45:31 UTC
Permalink
Hi Hena,

Regarding stereo: Anaglyph and side-by-side will work on any monitor. Quadbuffered and Zalman (byrow) methods are hardware dependant. Nvidia supports quadbuffered only with Quadro cards, not with GeForce. Switch between stereo modes with the "Display > Stereo Mode" menu or with the command line:

PyMOL> stereo anaglyph
PyMOL> stereo crosseye
PyMOL> stereo quadbuffer
PyMOL> stereo byrow

Hope that helps.

Cheers,
Thomas
Post by Hena Dutta
Dear Pymol Users,
I installed pymol 1.7.2.1 in my laptop (windows 8.1) and found some errors. Please see the highlighted portion below.
How can I see stereo, although it has been enabled?
I installed Openbabel, but some plug-in are not being initialized.
Could you please suggest how can I solve these problems?
Best regards,
Hena
After running the program I found some
PyMOL(TM) Molecular Graphics System, Version 1.7.2.1.
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 <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 4.40.
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: GeForce GTX 670M/PCIe/SSE2
GL_VERSION: 4.4.0 NVIDIA 344.60
Detected 8 CPU cores. Enabled multithreaded rendering.
OpenGL quad-buffer stereo 3D detected and enabled.
Executive: Loading version 1.600 session...
Unable to initialize plugin 'mtsslDockGui' (pmg_tk.startup.mtsslDockGui).
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Optimize plug-in needs openbabel to be installed in your system, please follow the instructions at
http://openbabel.org/wiki/Get_Open_Babel
Unable to initialize plugin 'mtsslWizard' (pmg_tk.startup.mtsslWizard).
Unable to initialize plugin 'mtsslTrilaterate' (pmg_tk.startup.mtsslTrilaterate).
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
Loading...