pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Problem with Pymol 2.3.0 with 'undefined symbol: MMTF_unpack_from_string'

[Thomas H. <tho...@sc...>]

Hi Heng-Keat,

A "clean" build will probably fix this. It looks like you partially recompiled with --use-msgpackc=no?

To do a clean build: Remove the "build" directory and try again.

Cheers,
  Thomas


> On Feb 14, 2019, at 8:00 PM, Ta...@em... wrote:
> 
> Dear all,
> 
> I installed the pymol on my machine with Ubuntu 18.04.1 LTS. When I launch pymol and error appears:
> 
> Traceback (most recent call last):
>  File "/home/mauricetam/Documents/software/pymol-2.3.0//lib/python2.7/site-packages/pymol/__init__.py", line 64, in <module>
>    import pymol
>  File "/home/mauricetam/Documents/software/pymol-2.3.0/lib/python2.7/site-packages/pymol/__init__.py", line 580, in <module>
>    import pymol._cmd
> ImportError: /home/mauricetam/Documents/software/pymol-2.3.0/lib/python2.7/site-packages/pymol/_cmd.so: undefined symbol: MMTF_unpack_from_string
> 
> Any idea what is going wrong?
> 
> Thank you for your help.
> 
> Best
> Heng-Keat

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] Problem with Pymol 2.3.0 with 'undefined symbol: MMTF_unpack_from_string'

[<Ta...@em...>]

Dear all,

I installed the pymol on my machine with Ubuntu 18.04.1 LTS. When I  
launch pymol and error appears:

Traceback (most recent call last):
   File  
"/home/mauricetam/Documents/software/pymol-2.3.0//lib/python2.7/site-packages/pymol/__init__.py", line 64, in  
<module>
     import pymol
   File  
"/home/mauricetam/Documents/software/pymol-2.3.0/lib/python2.7/site-packages/pymol/__init__.py", line 580, in  
<module>
     import pymol._cmd
ImportError:  
/home/mauricetam/Documents/software/pymol-2.3.0/lib/python2.7/site-packages/pymol/_cmd.so: undefined symbol:  
MMTF_unpack_from_string

Any idea what is going wrong?

Thank you for your help.

Best
Heng-Keat

Re: [PyMOL] Problem with Open source Pymol 2.3.0 (missing external GUI)

[Thomas H. <tho...@sc...>]

Hi Heng-Keat,

Getting CCTBX to work with PyMOL is quite a journey. Please read:

https://pymolwiki.org/index.php/CCTBX#Open-Source_PyMOL

Cheers,
  Thomas

> On Feb 14, 2019, at 11:27 AM, Ta...@em... wrote:
> 
> Dear all,
> 
> After I reinstalled the pmw, it ran through and now it said 'no modules named _tkinter' as shown below:
> 
> Warning: GL_DRAW_BUFFER0=0 -> using GL_BACK
> Detected OpenGL version 3.0. Shaders available.
> Geometry shaders not available
> Detected GLSL version 1.30.
> OpenGL graphics engine:
>  GL_VENDOR:   Intel Open Source Technology Center
>  GL_RENDERER: Mesa DRI Intel(R) Haswell Mobile
>  GL_VERSION:  3.0 Mesa 18.2.8
> Traceback (most recent call last):
>  File "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/__init__.py", line 27, in run
>    from .PMGApp import PMGApp
>  File "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/PMGApp.py", line 22, in <module>
>    import Pmw
>  File "/home/mauricetam/software/cctbx/cctbx_plus_build/base/lib/python2.7/site-packages/Pmw.py", line 8, in <module>
> Detected 4 CPU cores.  Enabled multithreaded rendering.
>    import Tkinter as tkinter
>  File "/home/mauricetam/software/cctbx/cctbx_plus_build/base/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module>
>    import _tkinter # If this fails your Python may not be configured for Tk
> ImportError: No module named _tkinter
> 
> Thanks for the help.
> 
> Best
> HK
> 
> Quoting Ta...@em...:
> 
>> To whom it may concern,
>> 
>> I installed the pymol on my machine with Ubuntu 18.04.1 LTS
>> 
>> I have a problem with 'Qt not available, using GLUT/Tk interface' when install pymol with:
>> 
>> python setup.py install --prefix=/home/mauricetam/software/pymol-2.3.0/ --use-msgpackc=no
>> 
>> After I installed it with:
>> 
>> python setup.py install --prefix=/home/mauricetam/software/pymol-2.3.0/ --use-msgpackc=no --glut
>> 
>> Now, the problem is I don't see the external GUI and there is an error as shown below:
>> 
>> Warning: GL_DRAW_BUFFER0=0 -> using GL_BACK
>> Detected OpenGL version 3.0. Shaders available.
>> Geometry shaders not available
>> Detected GLSL version 1.30.
>> OpenGL graphics engine:
>>  GL_VENDOR:   Intel Open Source Technology Center
>>  GL_RENDERER: Mesa DRI Intel(R) Haswell Mobile
>>  GL_VERSION:  3.0 Mesa 18.2.2
>> Traceback (most recent call last):
>>  File "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/__init__.py", line 27, in run
>>    from .PMGApp import PMGApp
>>  File "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/PMGApp.py", line 22, in <module>
>>    import Pmw
>> ImportError: No module named Pmw
>> Detected 4 CPU cores.  Enabled multithreaded rendering.
>> 
>> Any idea what is going wrong on my machine?
>> 
>> Thank you for the help.
>> 
>> Best
>> Heng-Keat

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Problem with Open source Pymol 2.3.0 (missing external GUI)

[<Ta...@em...>]

Dear all,

After I reinstalled the pmw, it ran through and now it said 'no  
modules named _tkinter' as shown below:

Warning: GL_DRAW_BUFFER0=0 -> using GL_BACK
  Detected OpenGL version 3.0. Shaders available.
  Geometry shaders not available
  Detected GLSL version 1.30.
  OpenGL graphics engine:
   GL_VENDOR:   Intel Open Source Technology Center
   GL_RENDERER: Mesa DRI Intel(R) Haswell Mobile
   GL_VERSION:  3.0 Mesa 18.2.8
Traceback (most recent call last):
   File  
"/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/__init__.py", line 27, in  
run
     from .PMGApp import PMGApp
   File  
"/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/PMGApp.py", line 22, in  
<module>
     import Pmw
   File  
"/home/mauricetam/software/cctbx/cctbx_plus_build/base/lib/python2.7/site-packages/Pmw.py", line 8, in  
<module>
  Detected 4 CPU cores.  Enabled multithreaded rendering.
     import Tkinter as tkinter
   File  
"/home/mauricetam/software/cctbx/cctbx_plus_build/base/lib/python2.7/lib-tk/Tkinter.py", line 39, in  
<module>
     import _tkinter # If this fails your Python may not be configured for Tk
ImportError: No module named _tkinter

Thanks for the help.

Best
HK

Quoting Ta...@em...:

> To whom it may concern,
>
> I installed the pymol on my machine with Ubuntu 18.04.1 LTS
>
> I have a problem with 'Qt not available, using GLUT/Tk interface'  
> when install pymol with:
>
> python setup.py install  
> --prefix=/home/mauricetam/software/pymol-2.3.0/ --use-msgpackc=no
>
> After I installed it with:
>
> python setup.py install  
> --prefix=/home/mauricetam/software/pymol-2.3.0/ --use-msgpackc=no  
> --glut
>
> Now, the problem is I don't see the external GUI and there is an  
> error as shown below:
>
> Warning: GL_DRAW_BUFFER0=0 -> using GL_BACK
>  Detected OpenGL version 3.0. Shaders available.
>  Geometry shaders not available
>  Detected GLSL version 1.30.
>  OpenGL graphics engine:
>   GL_VENDOR:   Intel Open Source Technology Center
>   GL_RENDERER: Mesa DRI Intel(R) Haswell Mobile
>   GL_VERSION:  3.0 Mesa 18.2.2
> Traceback (most recent call last):
>   File  
> "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/__init__.py", line 27, in  
> run
>     from .PMGApp import PMGApp
>   File  
> "/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/PMGApp.py", line 22, in  
> <module>
>     import Pmw
> ImportError: No module named Pmw
>  Detected 4 CPU cores.  Enabled multithreaded rendering.
>
> Any idea what is going wrong on my machine?
>
> Thank you for the help.
>
> Best
> Heng-Keat
>
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:  
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Problem with Open source Pymol 2.3.0 (missing external GUI)

[<Ta...@em...>]

To whom it may concern,

I installed the pymol on my machine with Ubuntu 18.04.1 LTS

I have a problem with 'Qt not available, using GLUT/Tk interface' when  
install pymol with:

python setup.py install  
--prefix=/home/mauricetam/software/pymol-2.3.0/ --use-msgpackc=no

After I installed it with:

python setup.py install  
--prefix=/home/mauricetam/software/pymol-2.3.0/ --use-msgpackc=no --glut

Now, the problem is I don't see the external GUI and there is an error  
as shown below:

Warning: GL_DRAW_BUFFER0=0 -> using GL_BACK
  Detected OpenGL version 3.0. Shaders available.
  Geometry shaders not available
  Detected GLSL version 1.30.
  OpenGL graphics engine:
   GL_VENDOR:   Intel Open Source Technology Center
   GL_RENDERER: Mesa DRI Intel(R) Haswell Mobile
   GL_VERSION:  3.0 Mesa 18.2.2
Traceback (most recent call last):
   File  
"/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/__init__.py", line 27, in  
run
     from .PMGApp import PMGApp
   File  
"/home/mauricetam/software/pymol-2.3.0/lib/python2.7/site-packages/pmg_tk/PMGApp.py", line 22, in  
<module>
     import Pmw
ImportError: No module named Pmw
  Detected 4 CPU cores.  Enabled multithreaded rendering.

Any idea what is going wrong on my machine?

Thank you for the help.

Best
Heng-Keat

Re: [PyMOL] PyMOL 2.3 released

[Jack V. <ja...@ma...>]

Thank you

From: Jarrett Johnson <jar...@sc...>
Date: Wednesday, February 13, 2019 at 10:36 AM
To: Jack Vizelter <ja...@ma...>
Cc: Thomas Holder <tho...@sc...>, Pymol User list <pym...@li...>
Subject: Re: [PyMOL] PyMOL 2.3 released

Hi Jack,

We've tested with Mojave since its release and have found no issues.

Jarrett J.

On Tue, Feb 12, 2019 at 12:51 PM Jack Vizelter <ja...@ma...<mailto:ja...@ma...>> wrote:
Hi,

Is this version supported under macOS 10.14.x (Mojave)?   The supported OS listing just says 10.9+ but wanted to confirm.

Thnx,
-jack

-----Original Message-----
From: Thomas Holder <tho...@sc...<mailto:tho...@sc...>>
Date: Monday, February 11, 2019 at 10:54 AM
To: Pymol User list <pym...@li...<mailto:pym...@li...>>
Subject: [PyMOL] PyMOL 2.3 released

    Greetings,

    We are happy to announce the release of PyMOL 2.3. Download ready-to-use bundles from https://urldefense.proofpoint.com/v2/url?u=https-3A__pymol.org_&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=M9y4i1kkzjJaykmXjFMEB8nDyvQFZ-_3sHaRTTi-rec&e= or update your installation with "conda install -c schrodinger pymol".

    New features include:
    - Atom-level cartoon transparency
    - Fast MMTF export
    - Sequence viewer gaps display

    This is the first time that we provide PyMOL bundles with Python 3. If you use custom or third-party Python 2 scripts, they might stop working until you convert them (e.g. using a converter tool like 2to3).

    Find the complete release notes at:
    https://urldefense.proofpoint.com/v2/url?u=https-3A__pymol.org_d_media-3Anew23&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=DdMiFFA3kJDoelX1qbJz9t9flE6G53M33MEdaZkRSzA&e=

    We welcome any feedback and bug reports.

    Cheers,
    - The PyMOL Team at Schrödinger

    --
    Thomas Holder
    PyMOL Principal Developer
    Schrödinger, Inc.

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_______________________________________________
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--
Jarrett Johnson
PyMOL Developer
Schrödinger, Inc.

Re: [PyMOL] PyMOL 2.3.0/CentOS-7: Qt not available, using GLUT/Tk interface ?

[Tru H. <tr...@pa...>]

On Wed, Feb 13, 2019 at 05:53:33PM +0100, Thomas Holder wrote:
> Don't split "build" and "install" (or pass --glut to both calls):
> 
>     python setup.py --glut build install --prefix=...
that just works :D

Thanks

Tru

-- 
Dr Tru Huynh | mailto:tr...@pa... | tel +33 1 45 68 87 37
https://research.pasteur.fr/en/team/structural-bioinformatics/
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  

Re: [PyMOL] PyMOL 2.3.0/CentOS-7: Qt not available, using GLUT/Tk interface ?

[Thomas H. <tho...@sc...>]

Don't split "build" and "install" (or pass --glut to both calls):

    python setup.py --glut build install --prefix=...

Cheers,
  Thomas

> On Feb 13, 2019, at 5:44 PM, Tru Huynh <tr...@pa...> wrote:
> 
> On Wed, Feb 13, 2019 at 05:21:09PM +0100, Tru Huynh wrote:
> ...
>> 
>> Trying to install PyQt4_gpl_x11-4.12. on CentOS-7 is another issue :)
>> ...
>> 
> 
> I went the easy route and pip3 install PyQt5-sip PyQt5,
> and rebuild ...
> 
> the Python-3.5.2 version now works fine, but not the Python-3.6.6
> which still fails!
> 
> [tru@sillage ~]$ module add pymol/release/2.3.0-Python-3.5.2 
> [tru@sillage ~]$ pymol
> PyMOL(TM) Molecular Graphics System, Version 2.3.0.
> 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 <command-name>" for information on a specific command.
> 
> Hit ESC anytime to toggle between text and graphics.
> 
> Detected OpenGL version 4.6. Shaders available.
> Detected GLSL version 4.60.
> OpenGL graphics engine:
>  GL_VENDOR:   NVIDIA Corporation
>  GL_RENDERER: GeForce GT 1030/PCIe/SSE2
>  GL_VERSION:  4.6.0 NVIDIA 410.93
> Detected 6 CPU cores.  Enabled multithreaded rendering.
> 
> 
> [tru@sillage ~]$ module add pymol/release/2.3.0-Python-3.6.6
> [tru@sillage ~]$ pymol
> Traceback (most recent call last):
>  File "/c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/__init__.py", line 64, in <module>
>    import pymol
>  File "/c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/__init__.py", line 580, in <module>
>    import pymol._cmd
> ImportError: /c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/_cmd.cpython-36m-x86_64-linux-gnu.so: undefined symbol: glutSwapBuffers
> 
> Cheers
> 
> Tru
> -- 
> Dr Tru Huynh | mailto:tr...@pa... | tel +33 1 45 68 87 37
> https://research.pasteur.fr/en/team/structural-bioinformatics/
> Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] PyMOL 2.3.0/CentOS-7: Qt not available, using GLUT/Tk interface ?

[Tru H. <tr...@pa...>]

On Wed, Feb 13, 2019 at 05:21:09PM +0100, Tru Huynh wrote:
...
> 
> Trying to install PyQt4_gpl_x11-4.12. on CentOS-7 is another issue :)
> ...
> 

I went the easy route and pip3 install PyQt5-sip PyQt5,
and rebuild ...

the Python-3.5.2 version now works fine, but not the Python-3.6.6
which still fails!

[tru@sillage ~]$ module add pymol/release/2.3.0-Python-3.5.2 
[tru@sillage ~]$ pymol
 PyMOL(TM) Molecular Graphics System, Version 2.3.0.
 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 <command-name>" for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Detected OpenGL version 4.6. Shaders available.
 Detected GLSL version 4.60.
 OpenGL graphics engine:
  GL_VENDOR:   NVIDIA Corporation
  GL_RENDERER: GeForce GT 1030/PCIe/SSE2
  GL_VERSION:  4.6.0 NVIDIA 410.93
 Detected 6 CPU cores.  Enabled multithreaded rendering.


[tru@sillage ~]$ module add pymol/release/2.3.0-Python-3.6.6
[tru@sillage ~]$ pymol
Traceback (most recent call last):
  File "/c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/__init__.py", line 64, in <module>
    import pymol
  File "/c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/__init__.py", line 580, in <module>
    import pymol._cmd
ImportError: /c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/_cmd.cpython-36m-x86_64-linux-gnu.so: undefined symbol: glutSwapBuffers

Cheers

Tru
-- 
Dr Tru Huynh | mailto:tr...@pa... | tel +33 1 45 68 87 37
https://research.pasteur.fr/en/team/structural-bioinformatics/
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  

Re: [PyMOL] PyMOL 2.3.0/CentOS-7: Qt not available, using GLUT/Tk interface ?

[Tru H. <tr...@pa...>]

Hi Thomas,

On Wed, Feb 13, 2019 at 04:28:10PM +0100, Thomas Holder wrote:
> Hi Tru,
> 
> There is one thing we changed: The legacy GLUT support is not enabled by default anymore. If that's the issue here, you have two options:
> 
> 1) install PyQt (recommended)
> 2) or compile PyMOL with --glut

I am trying the --glut way and that fixed the Python/2.7.15 build
and run fine, thanks!

	python setup.py --glut  build 
	python setup.py install --prefix=...

[tru@sillage ~]$ module add pymol/release/2.3.0-Python-2.7.15 
[tru@sillage ~]$ pymol
Qt not available, using GLUT/Tk interface
 PyMOL(TM) Molecular Graphics System, Version 2.3.0.
 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 <command-name>" for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

Warning: GL_DRAW_BUFFER0=0 -> using GL_BACK
 Detected OpenGL version 4.6. Shaders available.
 Detected GLSL version 4.60.
 OpenGL graphics engine:
  GL_VENDOR:   NVIDIA Corporation
  GL_RENDERER: GeForce GT 1030/PCIe/SSE2
  GL_VERSION:  4.6.0 NVIDIA 410.93
 Detected 6 CPU cores.  Enabled multithreaded rendering.

PyMOL>viewport 640,480
Plugin 'lightingsettings_gui' only available with PyQt GUI.
...

But the same build option fails for both Python/3.5.2 and 3.6.6 with:
[tru@sillage ~]$ pymol
Traceback (most recent call last):
  File "/c7/shared/pymol/release/2.3.0-Python-3.5.2/lib/python3.5/site-packages/pymol/__init__.py", line 64, in <module>
    import pymol
  File "/c7/shared/pymol/release/2.3.0-Python-3.5.2/lib/python3.5/site-packages/pymol/__init__.py", line 580, in <module>
    import pymol._cmd
ImportError: /c7/shared/pymol/release/2.3.0-Python-3.5.2/lib/python3.5/site-packages/pymol/_cmd.cpython-35m-x86_64-linux-gnu.so: undefined symbol: glutSwapBuffers

Traceback (most recent call last):
  File "/c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/__init__.py", line 64, in <module>
    import pymol
  File "/c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/__init__.py", line 580, in <module>
    import pymol._cmd
ImportError: /c7/shared/pymol/release/2.3.0-Python-3.6.6/lib/python3.6/site-packages/pymol/_cmd.cpython-36m-x86_64-linux-gnu.so: undefined symbol: glutSwapBuffers

Trying to install PyQt4_gpl_x11-4.12. on CentOS-7 is another issue :)
[tru@borma PyQt4_gpl_x11-4.12.3]$ python3 configure-ng.py  --confirm-license --destdir /dev/shm/PyQt4_gpl_x11-4.12.3 --qmake=/usr/lib64/qt4/bin/qmake
Querying qmake about your Qt installation...
Determining the details of your Qt installation...
This is the GPL version of PyQt 4.12.3 (licensed under the GNU General Public
License) for Python 3.6.6 on linux.
Found the license file pyqt-gpl.sip.
Error: This version of PyQt4 requires sip 4.19.12 or later.
[tru@borma PyQt4_gpl_x11-4.12.3]$ rpm -qa sip\*
sip-macros-4.14.6-4.el7.x86_64
sip-devel-4.14.6-4.el7.x86_64
sip-4.14.6-4.el7.x86_64
...

Cheers

Tru
-- 
Dr Tru Huynh | mailto:tr...@pa... | tel +33 1 45 68 87 37
https://research.pasteur.fr/en/team/structural-bioinformatics/
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  

Re: [PyMOL] PyMOL 2.3 released

[Jarrett J. <jar...@sc...>]

Hi Jack,

We've tested with Mojave since its release and have found no issues.

Jarrett J.

On Tue, Feb 12, 2019 at 12:51 PM Jack Vizelter <ja...@ma...>
wrote:

> Hi,
>
> Is this version supported under macOS 10.14.x (Mojave)?   The supported OS
> listing just says 10.9+ but wanted to confirm.
>
> Thnx,
> -jack
>
> -----Original Message-----
> From: Thomas Holder <tho...@sc...>
> Date: Monday, February 11, 2019 at 10:54 AM
> To: Pymol User list <pym...@li...>
> Subject: [PyMOL] PyMOL 2.3 released
>
>     Greetings,
>
>     We are happy to announce the release of PyMOL 2.3. Download
> ready-to-use bundles from
> https://urldefense.proofpoint.com/v2/url?u=https-3A__pymol.org_&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=M9y4i1kkzjJaykmXjFMEB8nDyvQFZ-_3sHaRTTi-rec&e=
> or update your installation with "conda install -c schrodinger pymol".
>
>     New features include:
>     - Atom-level cartoon transparency
>     - Fast MMTF export
>     - Sequence viewer gaps display
>
>     This is the first time that we provide PyMOL bundles with Python 3. If
> you use custom or third-party Python 2 scripts, they might stop working
> until you convert them (e.g. using a converter tool like 2to3).
>
>     Find the complete release notes at:
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__pymol.org_d_media-3Anew23&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=DdMiFFA3kJDoelX1qbJz9t9flE6G53M33MEdaZkRSzA&e=
>
>     We welcome any feedback and bug reports.
>
>     Cheers,
>     - The PyMOL Team at Schrödinger
>
>     --
>     Thomas Holder
>     PyMOL Principal Developer
>     Schrödinger, Inc.
>
>     _______________________________________________
>     PyMOL-users mailing list
>     Archives:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=9y_R-PjUqUT6wzjEs1ECxF59shYPiWuYB_7fThlDadU&e=
>     Unsubscribe:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=WVkM4La4mZsWQ2beQpPA_hXCmu_AFvn6RbGtetuCDqA&e=
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 
Jarrett Johnson
PyMOL Developer
Schrödinger, Inc.

Re: [PyMOL] PyMOL 2.3.0/CentOS-7: Qt not available, using GLUT/Tk interface ?

[Thomas H. <tho...@sc...>]

Hi Tru,

There is one thing we changed: The legacy GLUT support is not enabled by default anymore. If that's the issue here, you have two options:

1) install PyQt (recommended)
2) or compile PyMOL with --glut

Cheers,
  Thomas


> On Feb 13, 2019, at 3:44 PM, Tru Huynh <tr...@pa...> wrote:
> 
> Hi,
> 
> I have some issue with the latest released version (2.3.0) and
> manually build Python 2.7.15, 3.5.2 and 3.6.6 on our CentOS-7 machines.
> 
> [tru@sillage ~]$ module add pymol/release/2.3.0-Python-3.6.6
> [tru@sillage ~]$ module li
> Currently Loaded Modulefiles:
>  1) Python/3.6.6                       3) pymol/release/2.3.0-Python-3.6.6
>  2) msgpack/2.1.5
> [tru@sillage ~]$ pymol
> Qt not available, using GLUT/Tk interface
> [tru@sillage ~]$ echo $?
> 0
> 
> The different Python versions are isolated through the environment
> modules and the issue has only appeared with 2.3.0 and all the python
> versions except the version using the system provided python version.
> 
> these fails:
> pymol/release/2.3.0-Python-2.7.15  pymol/release/2.3.0-Python-3.6.6
> pymol/release/2.3.0-Python-3.5.2 
> 
> this works:
> pymol/release/2.3.0-Python-centos7
> 
> [tru@sillage ~]$ module add pymol/release/2.3.0-Python-centos7
> [tru@sillage ~]$ pymol
> PyMOL(TM) Molecular Graphics System, Version 2.3.0.
> 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 <command-name>" for information on a specific command.
> 
> Hit ESC anytime to toggle between text and graphics.
> 
> Detected OpenGL version 4.6. Shaders available.
> Detected GLSL version 4.60.
> OpenGL graphics engine:
>  GL_VENDOR:   NVIDIA Corporation
>  GL_RENDERER: GeForce GT 1030/PCIe/SSE2
>  GL_VERSION:  4.6.0 NVIDIA 410.93
> Detected 6 CPU cores.  Enabled multithreaded rendering.
> 
> and all the previous versions of pymol are perfectly fine...
> 
> pymol/release/1.8.7-Python-2.7.12  pymol/release/2.1.0-Python-3.6.6
> pymol/release/1.8.7-Python-2.7.15  pymol/release/2.1.0-Python-centos7
> pymol/release/1.8.7-Python-3.5.2   pymol/release/2.2.0-Python-2.7.15
> pymol/release/1.8.7-Python-3.6.3   pymol/release/2.2.0-Python-3.5.2
> pymol/release/1.8.7-Python-3.6.6   pymol/release/2.2.0-Python-3.6.6
> pymol/release/1.8.7-Python-centos7 pymol/release/2.2.0-Python-centos7
> pymol/release/2.1.0-Python-2.7.12  
> pymol/release/2.1.0-Python-2.7.15  
> pymol/release/2.1.0-Python-3.5.2   
> pymol/release/2.1.0-Python-3.6.3   
> 
> Any idea where I can start looking at?
> 
> python3 build process details:
> module purge && module add Python/${PYTHON_V}
> python3 setup.py build
> python3 setup.py install --prefix=/....
> 
> for python2, I just resplaced python3 by python in the lines above.
> 
> Any idea what could be causing this behaviour?
> 
> Cheers
> 
> Tru
> 
> -- 
> Dr Tru Huynh | mailto:tr...@pa... | tel +33 1 45 68 87 37
> https://research.pasteur.fr/en/team/structural-bioinformatics/
> Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] PyMOL 2.3.0/CentOS-7: Qt not available, using GLUT/Tk interface ?

[Tru H. <tr...@pa...>]

Hi,

I have some issue with the latest released version (2.3.0) and
manually build Python 2.7.15, 3.5.2 and 3.6.6 on our CentOS-7 machines.

[tru@sillage ~]$ module add pymol/release/2.3.0-Python-3.6.6
[tru@sillage ~]$ module li
Currently Loaded Modulefiles:
  1) Python/3.6.6                       3) pymol/release/2.3.0-Python-3.6.6
  2) msgpack/2.1.5
[tru@sillage ~]$ pymol
Qt not available, using GLUT/Tk interface
[tru@sillage ~]$ echo $?
0

The different Python versions are isolated through the environment
modules and the issue has only appeared with 2.3.0 and all the python
versions except the version using the system provided python version.

these fails:
pymol/release/2.3.0-Python-2.7.15  pymol/release/2.3.0-Python-3.6.6
pymol/release/2.3.0-Python-3.5.2 

this works:
pymol/release/2.3.0-Python-centos7

[tru@sillage ~]$ module add pymol/release/2.3.0-Python-centos7
[tru@sillage ~]$ pymol
 PyMOL(TM) Molecular Graphics System, Version 2.3.0.
 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 <command-name>" for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Detected OpenGL version 4.6. Shaders available.
 Detected GLSL version 4.60.
 OpenGL graphics engine:
  GL_VENDOR:   NVIDIA Corporation
  GL_RENDERER: GeForce GT 1030/PCIe/SSE2
  GL_VERSION:  4.6.0 NVIDIA 410.93
 Detected 6 CPU cores.  Enabled multithreaded rendering.

and all the previous versions of pymol are perfectly fine...

pymol/release/1.8.7-Python-2.7.12  pymol/release/2.1.0-Python-3.6.6
pymol/release/1.8.7-Python-2.7.15  pymol/release/2.1.0-Python-centos7
pymol/release/1.8.7-Python-3.5.2   pymol/release/2.2.0-Python-2.7.15
pymol/release/1.8.7-Python-3.6.3   pymol/release/2.2.0-Python-3.5.2
pymol/release/1.8.7-Python-3.6.6   pymol/release/2.2.0-Python-3.6.6
pymol/release/1.8.7-Python-centos7 pymol/release/2.2.0-Python-centos7
pymol/release/2.1.0-Python-2.7.12  
pymol/release/2.1.0-Python-2.7.15  
pymol/release/2.1.0-Python-3.5.2   
pymol/release/2.1.0-Python-3.6.3   

Any idea where I can start looking at?

python3 build process details:
module purge && module add Python/${PYTHON_V}
python3 setup.py build
python3 setup.py install --prefix=/....

for python2, I just resplaced python3 by python in the lines above.

Any idea what could be causing this behaviour?

Cheers

Tru

-- 
Dr Tru Huynh | mailto:tr...@pa... | tel +33 1 45 68 87 37
https://research.pasteur.fr/en/team/structural-bioinformatics/
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  

[PyMOL] 3d monitor recommendation?

[Bruce O. <bco...@gm...>]

Dear all,

I used to use PyMol with a fast refreshing CRT and page flipping, but the
monitor has died.....

What would you buy if you had $2,000 to replace it?

Just a new monitor?

Or any VR supported, maybe with an interface other than mice?

Thanks!

Bruce

Re: [PyMOL] PyMOL 2.3 released

[Jack V. <ja...@ma...>]

Hi,

Is this version supported under macOS 10.14.x (Mojave)?   The supported OS listing just says 10.9+ but wanted to confirm.

Thnx,
-jack

-----Original Message-----
From: Thomas Holder <tho...@sc...>
Date: Monday, February 11, 2019 at 10:54 AM
To: Pymol User list <pym...@li...>
Subject: [PyMOL] PyMOL 2.3 released

    Greetings,
    
    We are happy to announce the release of PyMOL 2.3. Download ready-to-use bundles from https://urldefense.proofpoint.com/v2/url?u=https-3A__pymol.org_&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=M9y4i1kkzjJaykmXjFMEB8nDyvQFZ-_3sHaRTTi-rec&e= or update your installation with "conda install -c schrodinger pymol".
    
    New features include:
    - Atom-level cartoon transparency
    - Fast MMTF export
    - Sequence viewer gaps display
    
    This is the first time that we provide PyMOL bundles with Python 3. If you use custom or third-party Python 2 scripts, they might stop working until you convert them (e.g. using a converter tool like 2to3).
    
    Find the complete release notes at:
    https://urldefense.proofpoint.com/v2/url?u=https-3A__pymol.org_d_media-3Anew23&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=DdMiFFA3kJDoelX1qbJz9t9flE6G53M33MEdaZkRSzA&e= 
    
    We welcome any feedback and bug reports.
    
    Cheers,
    - The PyMOL Team at Schrödinger
    
    --
    Thomas Holder
    PyMOL Principal Developer
    Schrödinger, Inc.
    
    _______________________________________________
    PyMOL-users mailing list
    Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=9y_R-PjUqUT6wzjEs1ECxF59shYPiWuYB_7fThlDadU&e=
    Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=uZ7OTQ4NzBWkCWuelwpsqn3NhvXJQHUkEFDh1s3GqrM&m=EdVxNaXoTBbrFjOSxSGtf80f5GLwY4UoeoqXOgi2y1Y&s=WVkM4La4mZsWQ2beQpPA_hXCmu_AFvn6RbGtetuCDqA&e=

Re: [PyMOL] dark structure

[sunting <sx...@lb...>]

Hi Cyprian and Thomas, 

Problem solved! Thanks!

Sunting 

Sent from Mail for Windows 10

From: Thomas Holder
Sent: Tuesday, February 12, 2019 1:30 AM
To: Cyprian Cukier
Cc: sunting; pym...@li...
Subject: Re: [PyMOL] dark structure

Hi Cyprian and Sunting,

Better solutions:

- put "set precomputed_lighting" in your pymolrc
- or just upgrade to PyMOL 2.3 (has precomputed_lighting on by default)

See also:
https://github.com/schrodinger/pymol-open-source/issues/15
https://sourceforge.net/p/pymol/mailman/message/36455017/

Cheers,
  Thomas

> On Feb 12, 2019, at 9:54 AM, Cyprian Cukier <cyp...@se...> wrote:
> 
> Hi Sunting,
>  
> Just need to turn off shaders -> ‘set use_shaders, off’. Do not know how to switch off the default on.
>  
> Best,
> Cyprian
>  
> From: sunting <sx...@lb...> 
> Sent: Monday, February 11, 2019 7:20 PM
> To: pym...@li... <pym...@li...>
> Subject: [PyMOL] dark structure
>  
> Hi, 
>  
> Is there any one who knows why the structure look so dark in pymol (see attached)? I have tried re-install the software but doesn’t work. 
> Thanks
>  
> Sunting

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] dark structure

[Thomas H. <tho...@sc...>]

Hi Cyprian and Sunting,

Better solutions:

- put "set precomputed_lighting" in your pymolrc
- or just upgrade to PyMOL 2.3 (has precomputed_lighting on by default)

See also:
https://github.com/schrodinger/pymol-open-source/issues/15
https://sourceforge.net/p/pymol/mailman/message/36455017/

Cheers,
  Thomas

> On Feb 12, 2019, at 9:54 AM, Cyprian Cukier <cyp...@se...> wrote:
> 
> Hi Sunting,
>  
> Just need to turn off shaders -> ‘set use_shaders, off’. Do not know how to switch off the default on.
>  
> Best,
> Cyprian
>  
> From: sunting <sx...@lb...> 
> Sent: Monday, February 11, 2019 7:20 PM
> To: pym...@li... <pym...@li...>
> Subject: [PyMOL] dark structure
>  
> Hi, 
>  
> Is there any one who knows why the structure look so dark in pymol (see attached)? I have tried re-install the software but doesn’t work. 
> Thanks
>  
> Sunting

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] NameError: name 'util' is not defined

[Søren N. <sor...@gm...>]

Hi Thomas,

I tried the wrapper, but it seems it only works once when you change the
color. If you try to change again I get this error:

Selector-Error: Invalid selection name "BSA_mono".
BSA_mono<--

BSA_mono being my loaded filename of course.... I can do other operations,
but coloring does not work.

Any suggestions?

Best,
Soren





On Tue, Feb 12, 2019 at 9:11 AM Thomas Holder <tho...@sc...>
wrote:

> Hi Soren,
>
> Very interesting script, thanks for sharing!
>
> It looks like pymol2.PyMOL() doesn't work with the util module. It would
> need to wrap all util functions and pass the "_self" argument with every
> function call, just like pymol2.cmd2.Cmd does.
>
> It works for me if I use pymol2.SingletonPyMOL() instead. That's what we
> use with the PyQt interface. This "singleton" version uses the global
> pymol.cmd and pymol.util modules as the API. You can only have one instance
> of the singleton.
>
> If you want multiple instances with pymol2.PyMOL(), you'll need to do the
> wrapping. For example like this:
>
> class SelfProxy:
>     def __init__(self, proxied, _self):
>         self._self = _self
>         self.proxied = proxied
>     def __getattr__(self, key):
>         v = getattr(self.proxied, key)
>         def wrapper(*a, **k):
>             k['_self'] = self._self
>             return v(*a, **k)
>         return wrapper
>
> # and after "self._pymol.start()":
>         import pymol.util
>         self._pymol.util = SelfProxy(pymol.util, self._pymol.cmd)
>
> I've tested this and it works with the color menu.
>
> Cheers,
>   Thomas
>
> > On Feb 12, 2019, at 8:26 AM, Søren Nielsen <sor...@gm...>
> wrote:
> >
> >
> > Hi,
> >
> > I am using pymol with a wxpython interface and everything seems to work,
> except when I try to change the color of an object using the internal gui,
> I get a NameError: name 'util' is not defined error... can you see what is
> the problem here?
> >
> > Best,
> > Soren
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Re: [PyMOL] dark structure

[Cyprian C. <cyp...@se...>]

Hi Sunting,

 

Just need to turn off shaders -> ‘set use_shaders, off’. Do not know how to switch off the default on.

 

Best,

Cyprian

 

From: sunting <sx...@lb...> 
Sent: Monday, February 11, 2019 7:20 PM
To: pym...@li... <pym...@li...>
Subject: [PyMOL] dark structure

 

Hi, 

 

Is there any one who knows why the structure look so dark in pymol (see attached)? I have tried re-install the software but doesn’t work. 

Thanks

 

Sunting

 

Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986>  for Windows 10

 

Re: [PyMOL] NameError: name 'util' is not defined

[Søren N. <sor...@gm...>]

Thanks for the quick answer Thomas!

Yes, I will need multiple instances so I will work with the proxy then.

Best,
Soren

On Tue, Feb 12, 2019 at 9:11 AM Thomas Holder <tho...@sc...>
wrote:

> Hi Soren,
>
> Very interesting script, thanks for sharing!
>
> It looks like pymol2.PyMOL() doesn't work with the util module. It would
> need to wrap all util functions and pass the "_self" argument with every
> function call, just like pymol2.cmd2.Cmd does.
>
> It works for me if I use pymol2.SingletonPyMOL() instead. That's what we
> use with the PyQt interface. This "singleton" version uses the global
> pymol.cmd and pymol.util modules as the API. You can only have one instance
> of the singleton.
>
> If you want multiple instances with pymol2.PyMOL(), you'll need to do the
> wrapping. For example like this:
>
> class SelfProxy:
>     def __init__(self, proxied, _self):
>         self._self = _self
>         self.proxied = proxied
>     def __getattr__(self, key):
>         v = getattr(self.proxied, key)
>         def wrapper(*a, **k):
>             k['_self'] = self._self
>             return v(*a, **k)
>         return wrapper
>
> # and after "self._pymol.start()":
>         import pymol.util
>         self._pymol.util = SelfProxy(pymol.util, self._pymol.cmd)
>
> I've tested this and it works with the color menu.
>
> Cheers,
>   Thomas
>
> > On Feb 12, 2019, at 8:26 AM, Søren Nielsen <sor...@gm...>
> wrote:
> >
> >
> > Hi,
> >
> > I am using pymol with a wxpython interface and everything seems to work,
> except when I try to change the color of an object using the internal gui,
> I get a NameError: name 'util' is not defined error... can you see what is
> the problem here?
> >
> > Best,
> > Soren
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Re: [PyMOL] NameError: name 'util' is not defined

[Thomas H. <tho...@sc...>]

Hi Soren,

Very interesting script, thanks for sharing!

It looks like pymol2.PyMOL() doesn't work with the util module. It would need to wrap all util functions and pass the "_self" argument with every function call, just like pymol2.cmd2.Cmd does.

It works for me if I use pymol2.SingletonPyMOL() instead. That's what we use with the PyQt interface. This "singleton" version uses the global pymol.cmd and pymol.util modules as the API. You can only have one instance of the singleton.

If you want multiple instances with pymol2.PyMOL(), you'll need to do the wrapping. For example like this:

class SelfProxy:
    def __init__(self, proxied, _self):
        self._self = _self
        self.proxied = proxied
    def __getattr__(self, key):
        v = getattr(self.proxied, key)
        def wrapper(*a, **k):
            k['_self'] = self._self
            return v(*a, **k)
        return wrapper

# and after "self._pymol.start()":
        import pymol.util
        self._pymol.util = SelfProxy(pymol.util, self._pymol.cmd)

I've tested this and it works with the color menu.

Cheers,
  Thomas

> On Feb 12, 2019, at 8:26 AM, Søren Nielsen <sor...@gm...> wrote:
> 
> 
> Hi,
> 
> I am using pymol with a wxpython interface and everything seems to work, except when I try to change the color of an object using the internal gui, I get a NameError: name 'util' is not defined error... can you see what is the problem here?
> 
> Best,
> Soren

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] NameError: name 'util' is not defined

[Søren N. <sor...@gm...>]

Hi,

I am using pymol with a wxpython interface and everything seems to work,
except when I try to change the color of an object using the internal gui,
I get a NameError: name 'util' is not defined error... can you see what is
the problem here?

Best,
Soren

Here is the script I am using:

import wx
from wx.glcanvas import GLCanvas
import OpenGL.GL as OGL
import pymol2

class PyMOLCanvas(GLCanvas):
    def __init__(self, parent):
        GLCanvas.__init__(self, parent,-1,
attribList=[wx.glcanvas.WX_GL_DOUBLEBUFFER, wx.glcanvas.WX_GL_RGBA])

        self.context = wx.glcanvas.GLContext(self)

        wx.EVT_PAINT(self, self.OnPaint)
        wx.EVT_SIZE(self, self.OnSize)
        wx.EVT_MOTION(self, self.OnMouseMotion)
        wx.EVT_RIGHT_DOWN(self, self.OnMouseDown)
        wx.EVT_RIGHT_UP(self, self.OnMouseUp)
        wx.EVT_LEFT_DOWN(self, self.OnMouseDown)
        wx.EVT_LEFT_UP(self, self.OnMouseUp)
        wx.EVT_MIDDLE_DOWN(self, self.OnMouseDown)
        wx.EVT_MIDDLE_UP(self, self.OnMouseUp)
        wx.EVT_MOUSEWHEEL(self, self.OnMouseWheel)

        self.button_map = {wx.MOUSE_BTN_LEFT:0, wx.MOUSE_BTN_MIDDLE:1,
wx.MOUSE_BTN_RIGHT:2}

        self.InitGL()
        self.LoadMolFile("C:/Programming/RAW/BSA_mono.pdb")

    def OnPaint(self, event):
        self.SetCurrent(self.context)
        width, height = self.GetSize()

        try:
            OGL.glViewport(0, 0, width, height)
            self._pymol.idle()
            self._pymol.draw()

            self.SwapBuffers()
        except Exception:
            pass

    def InitGL(self):
        self._pymol = pymol2.PyMOL()
        self._pymol.start()

        width, height = self.GetSize()
        self._pymol.reshape(width, height)

        self.PymolProcess()

    def OnSize(self, event):
        try:
            width, height = event.GetSize()
        except:
            width = event.GetSize().width
            height = event.GetSize().height

        try:
           self._pymol.reshape(width, height, True)
           self.PymolProcess()
        except AttributeError, e:
            print 'GL not init yet'

        self.Refresh()
        self.Update()

    def PymolProcess(self):
        self._pymol.idle()
        self.Refresh()
        self.Update()

    def OnMouseMotion(self, event):
        width, height = self.GetSize()

        self._pymol.drag(event.GetX(), height - event.GetY(), 0)
        self.PymolProcess()
        event.Skip()

    def OnMouseDown(self, event):
        width, height = self.GetSize()
        self._pymol.button(self.button_map[event.GetButton()], 0,
event.GetX(), height - event.GetY(), 0)
        self.PymolProcess()
        event.Skip()

    def OnMouseUp(self, event):
        width, height = self.GetSize()
        self._pymol.button(self.button_map[event.GetButton()], 1,
event.GetX(), height - event.GetY(), 0)
        self.PymolProcess()
        event.Skip()

    def OnMouseWheel(self, event):
        button = 4 if event.GetWheelRotation() > 0 else 3
        self._pymol.button(button, 0, event.GetX(), event.GetY(), 0)
        self.PymolProcess()
        event.Skip()

    def LoadMolFile(self, mol_file):
        self._pymol.cmd.load(str(mol_file))

class PyMOLPanel(wx.Panel):

    def __init__(self, parent, panel_id, name, enable_gui = False, *args,
**kwargs):
        wx.Panel.__init__(self, parent, panel_id, *args, name = name,
**kwargs)
        self._createLayout()

    def _createLayout(self):
        self.canvas = PyMOLCanvas(self)
        sizer = wx.BoxSizer(wx.VERTICAL)
        sizer.Add(self.canvas, 1, wx.ALL | wx.GROW)
        self.SetSizerAndFit(sizer)

if __name__ == '__main__':
    app = wx.App()
    frame = wx.Frame(None, -1, 'PyMol', wx.DefaultPosition,
wx.Size(400,400))
    canvas = PyMOLCanvas(frame)

    frame.Show()
    app.MainLoop()

Re: [PyMOL] PyMOL 2.3 released

[<s.m...@sb...>]

Thomas

Good job.  I just compiled and installed it in Debian Stretch in a VirtualBox (getting ready to update my main Linux platform)'

Went very smoothly with no problems.

Keep up the good work.

Regards,

		Steve

Stephen P. Molnar, Ph.D.
www.molecular-modling.net
(614)312-7528 (c)
Skype:  smolnar1

-----Original Message-----
From: Thomas Holder <tho...@sc...> 
Sent: Monday, February 11, 2019 10:31 AM
To: Pymol User list <pym...@li...>
Subject: [PyMOL] PyMOL 2.3 released

Greetings,

We are happy to announce the release of PyMOL 2.3. Download ready-to-use bundles from https://pymol.org/ or update your installation with "conda install -c schrodinger pymol".

New features include:
- Atom-level cartoon transparency
- Fast MMTF export
- Sequence viewer gaps display

This is the first time that we provide PyMOL bundles with Python 3. If you use custom or third-party Python 2 scripts, they might stop working until you convert them (e.g. using a converter tool like 2to3).

Find the complete release notes at:
https://pymol.org/d/media:new23 

We welcome any feedback and bug reports.

Cheers,
- The PyMOL Team at Schrödinger

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

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[PyMOL] dark structure

[sunting <sx...@lb...>]

Hi, 

Is there any one who knows why the structure look so dark in pymol (see attached)? I have tried re-install the software but doesn’t work. 
Thanks

Sunting

Sent from Mail for Windows 10

Re: [PyMOL] Reference point shifts when display screen is changed

[Thomas H. <tho...@sc...>]

Hi Gyan,

I think this issue has been fixed (in PyMOL 2.2.2). Can you please upgrade to the latest version?

Cheers,
  Thomas

> On Feb 9, 2019, at 11:35 PM, Gyanendra Kumar <gya...@bm...> wrote:
> 
> Hi there,
>  
> I am facing this problem of the reference point moving to a corner of the display window when I unplug the external monitor and the display moves to the MacBook screen, or when I connect another display e.g. a TV screen.
> Reset command or re-centering on an atom does not fix the problem and I end up closing pymol and having to restart the program.
>  
> Has anybody faced this problem and found a solution?
>  
> I am running pymol on MacOS Sierra Version 10.12.6. MacBook Pro 2017.
>  
> Thanks,
> Gyan

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.