pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] How to hide dihedral angle labels in mdo animation using set_dihedral

[Nanna H. L. <nh...@st...>]

Thank you very much Thomas!

Best, Nanna
________________________________
Fra: Thomas Holder <tho...@sc...>
Sendt: 25. februar 2020 03:00
Til: Nanna Holmgaard List <nh...@st...>
Cc: pym...@li... <pym...@li...>
Emne: Re: [PyMOL] How to hide dihedral angle labels in mdo animation using set_dihedral

Hi Nanna,

These indicators come from the various "pk" selections. The "unpick" command will remove them. Just call "unpick" right after "set_dihedral", like this:

mdo 30: set_dihedral sele1, sele2, sele3, sele4, 123; unpick

Hope that helps.

Cheers,
  Thomas

> On Feb 21, 2020, at 7:50 AM, Nanna Holmgaard List <nh...@st...> wrote:
>
> Dear PyMOL,
>
> I am using the set_dihedral command in an mdo animation of a dihedral rotation.
>
> In addition to rotating the bond, this command introduces three "labels":
> 1) dihedral angle label
> 2) dihedral angle indicator
> 3) circle around the bond, defining the central bond
>
> I want to have all three "labels" removed in my animation, but cannot figure out how to do it.
>
> So far, no matter what I tried the circle (3) always remains. I managed a dirty solution to move (1) and (2) outside the picture frame by the "set dihedral_size" and "set dihedral_label_position".
>
> I would much appreciate any suggestions to a solution, in particular removing the circle (3).
>
> Thank you very much in advance!
>
> Best, Nanna H. List
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] How to hide dihedral angle labels in mdo animation using set_dihedral

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

Hi Nanna,

These indicators come from the various "pk" selections. The "unpick" command will remove them. Just call "unpick" right after "set_dihedral", like this:

mdo 30: set_dihedral sele1, sele2, sele3, sele4, 123; unpick

Hope that helps.

Cheers,
  Thomas

> On Feb 21, 2020, at 7:50 AM, Nanna Holmgaard List <nh...@st...> wrote:
> 
> Dear PyMOL, 
> 
> I am using the set_dihedral command in an mdo animation of a dihedral rotation. 
> 
> In addition to rotating the bond, this command introduces three "labels":
> 1) dihedral angle label
> 2) dihedral angle indicator
> 3) circle around the bond, defining the central bond
> 
> I want to have all three "labels" removed in my animation, but cannot figure out how to do it.
> 
> So far, no matter what I tried the circle (3) always remains. I managed a dirty solution to move (1) and (2) outside the picture frame by the "set dihedral_size" and "set dihedral_label_position".
> 
> I would much appreciate any suggestions to a solution, in particular removing the circle (3).
> 
> Thank you very much in advance!
> 
> Best, Nanna H. List
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Accessing vertex normals from surface representation within PyMOL session

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

Hi Jared,

Apologies for the late reply. Unfortunately such an API doesn't exist. I agree that it would be very useful, I will file a feature request.

Cheers,
  Thomas

> On Feb 14, 2020, at 9:20 PM, Jared Sampson <jar...@co...> wrote:
> 
> Hi all -
> 
> Is it possible to access surface triangle mesh position and normal values on a per-selection basis within a PyMOL session?  I know it's possible to get these by writing out and parsing .obj files, but to do this for an entire protein surface in a per-atom/residue fashion would be inefficient.  I imagine there must be a function to access this similar to "dump" for isosurfaces, but haven't been able to find it.
> 
> Thanks a lot!
> 
> Cheers,
> Jared
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Pymol Rendering

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

Hi Seán,

Enabling multi-layer transparency should do the trick.

From the menu:
Setting > Transparency > Multi-Layer

From the command line:
PyMOL> set transparency_mode, 1

Hope that helps.

Cheers,
  Thomas


> On Feb 24, 2020, at 10:32 PM, Seán Downey <dow...@tc...> wrote:
> 
> Hi all, 
> 
> I am trying to render an image of a protein structure with a transparent surface and a slightly less transparent cartoon structure, of the same colour, in order to show both the cartoon structure and a ligand (non-transparent) bound within as well as the surface. Using the ray option, the ligand is visible, but the semi-transparent cartoon is not. Does anyone have any insight into this.  Note I am using version 2.2.3.
> 
> All the best,
> 
> Seán Downey 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] Pymol Rendering

[Seán D. <dow...@tc...>]

Hi all,

I am trying to render an image of a protein structure with a transparent
surface and a slightly less transparent cartoon structure, of the same
colour, in order to show both the cartoon structure and a ligand
(non-transparent) bound within as well as the surface. Using the ray
option, the ligand is visible, but the semi-transparent cartoon is not.
Does anyone have any insight into this.  Note I am using version 2.2.3.

All the best,

Seán Downey

[PyMOL] How to hide dihedral angle labels in mdo animation using set_dihedral

[Nanna H. L. <nh...@st...>]

Dear PyMOL,

I am using the set_dihedral command in an mdo animation of a dihedral rotation.

In addition to rotating the bond, this command introduces three "labels":
1) dihedral angle label
2) dihedral angle indicator
3) circle around the bond, defining the central bond

I want to have all three "labels" removed in my animation, but cannot figure out how to do it.

So far, no matter what I tried the circle (3) always remains. I managed a dirty solution to move (1) and (2) outside the picture frame by the "set dihedral_size" and "set dihedral_label_position".

I would much appreciate any suggestions to a solution, in particular removing the circle (3).

Thank you very much in advance!

Best, Nanna H. List

[PyMOL] Fw: How to compile pymol with --glut?

[sunyeping <sun...@al...>]

Using yum of centos or apt of Ubuntu cannot install the latest version.
------------------------------------------------------------------
From:Robi Gus <ro...@ma...>
Sent At:2020 Feb. 14 (Fri.) 22:00
To:孙业平 <sun...@al...>
Subject:Re: [PyMOL] How to compile pymol with --glut?

much easier to use apt to install open source pymol binaries
Sent: Friday, February 14, 2020 at 7:47 AM
From: "sunyeping via PyMOL-users" <pym...@li...>
To: "Thomas Holder" <tho...@sc...>
Cc: pymol-users <pym...@li...>
Subject: Re: [PyMOL] How to compile pymol with --glut?
Hi Thomas,
Thank you and I know this has been asked before, but following the suggestion posted by you does not solve the problem.
After run the two commands:
rm -rf build
python2 setup.py --glut install --prefix=~/pymol-install-py2
The same error still comes out.
------------------------------------------------------------------
From:Thomas Holder <tho...@sc...>
Sent At:2020 Feb. 11 (Tue.) 17:34
To:孙业平 <sun...@al...>
Cc:pymol-users <pym...@li...>
Subject:Re: [PyMOL] How to compile pymol with --glut?
 Hi Yeping,

 This has been asked before (by you :-)), see here:

https://sourceforge.net/p/pymol/mailman/message/36766620/

 Cheers,
   Thomas

 > On Feb 8, 2020, at 2:12 PM, 孙业平 via PyMOL-users <pym...@li...> wrote:
 > 
 > Dear pymol users,
 > 
 > I compiled pymol following the guide at https://pymolwiki.org/index.php/Linux_Install in my CentOS 8 system.
 > When I tried to launch pymol by the "./pymol" command, I got the following error:
 > 
 >     Qt not available, using GLUT/Tk interface
 > Traceback (most recent call last):
 >   File "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", line 65, in <module>
 >     pymol.launch(args)
 >   File "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", line 441, in launch
 >     _cmd.runpymol(_cmd._get_global_C_object(), block_input_hook)
 > NotImplementedError: compile with --glut
 > 
 > I then removed the "bin" and the "lib64" directories in the "pymol-open-source-build" directory and recompiled pymol with the following command:
 >        python3 setup --glut install --prefix=~/software/Pymol/pymol-open-source-build
 > 
 > However, the newly generated pymol binary file does not work either. Launch pymol give the same "Qt not available, using GLUT/Tk interface" error.
 > 
 > Could you help me with this?Thank you in advance.
 > 
 > Best regards.
 > 
 > 
 > _______________________________________________
 > PyMOL-users mailing list
 > Archives: http://www.mail-archive.com/pym...@li...
 > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

 --
 Thomas Holder
 PyMOL Principal Developer
 Schrödinger, Inc. 
 _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pym...@li... Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Accessing vertex normals from surface representation within PyMOL session

[Jared S. <jar...@co...>]

Hi all -

Is it possible to access surface triangle mesh position and normal values on a per-selection basis within a PyMOL session?  I know it's possible to get these by writing out and parsing .obj files, but to do this for an entire protein surface in a per-atom/residue fashion would be inefficient.  I imagine there must be a function to access this similar to "dump" for isosurfaces, but haven't been able to find it.

Thanks a lot!

Cheers,
Jared

[PyMOL] cmd.add_state_loop() function

[Zheng R. <zru...@gm...>]

Hi,

I'm trying to only add a given fraction of my structure ensemble to
the movie frames. I see that there is a "first" and "last" option in
the cmd.add_state_loop() function. However, the "last" option doesn't
seem to be used by the body of the cmd.add_state_loop() function (at
least the code in github). I guess this can be fixed easily?

Thank you!
Zheng

Re: [PyMOL] How to compile pymol with --glut?

[sunyeping <sun...@al...>]

Hi Thomas,

Thank you and I know this has been asked before, but following the suggestion posted by you does not solve the problem.

After run the two commands:
rm -rf build
python2 setup.py --glut install --prefix=~/pymol-install-py2

The same error still comes out.
------------------------------------------------------------------
From:Thomas Holder <tho...@sc...>
Sent At:2020 Feb. 11 (Tue.) 17:34
To:孙业平 <sun...@al...>
Cc:pymol-users <pym...@li...>
Subject:Re: [PyMOL] How to compile pymol with --glut?

Hi Yeping,

This has been asked before (by you :-)), see here:

https://sourceforge.net/p/pymol/mailman/message/36766620/

Cheers,
  Thomas

> On Feb 8, 2020, at 2:12 PM, 孙业平 via PyMOL-users <pym...@li...> wrote:
> 
> Dear pymol users,
> 
> I compiled pymol following the guide at https://pymolwiki.org/index.php/Linux_Install in my CentOS 8 system.
> When I tried to launch pymol by the "./pymol" command, I got the following error:
> 
>     Qt not available, using GLUT/Tk interface
> Traceback (most recent call last):
>   File "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", line 65, in <module>
>     pymol.launch(args)
>   File "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", line 441, in launch
>     _cmd.runpymol(_cmd._get_global_C_object(), block_input_hook)
> NotImplementedError: compile with --glut
> 
> I then removed the "bin" and the "lib64" directories in the "pymol-open-source-build" directory and recompiled pymol with the following command:
>        python3 setup --glut install --prefix=~/software/Pymol/pymol-open-source-build
> 
> However, the newly generated pymol binary file does not work either. Launch pymol give the same "Qt not available, using GLUT/Tk interface" error.
> 
> Could you help me with this?Thank you in advance.
> 
> Best regards.
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Can't install latest version on Mac

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

Hi Ioannis,

Can you provide some examples of the compiler error messages that you're
observing?

Jarrett J

On Thu, Feb 13, 2020 at 10:42 AM Ioannis Riziotis <riz...@eb...>
wrote:

> Hello,
>
> I have been trying to install the latest version of Pymol from GitHub on
> Catalina, following the compilation instructions in INSTALL. The process
> fails all the times, with lots of compilation warnings and errors.
> I have also used Homebrew, but the respective formula points to version
> 2.3.0 (
> https://github.com/schrodinger/pymol-open-source/archive/v2.3.0.tar.gz).
>
> Can you please give me some guidance on this? I need the latest version,
> because of some bugs in version 2.3.0
>
> Thank you,
> Ioannis
>
> --
> *Ioannis G. Riziotis*
> *PhD Fellow*
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>

[PyMOL] Can't install latest version on Mac

[Ioannis R. <riz...@eb...>]

Hello,

I have been trying to install the latest version of Pymol from GitHub on Catalina, following the compilation instructions in INSTALL. The process fails all the times, with lots of compilation warnings and errors.
I have also used Homebrew, but the respective formula points to version 2.3.0 (https://github.com/schrodinger/pymol-open-source/archive/v2.3.0.tar.gz <https://github.com/schrodinger/pymol-open-source/archive/v2.3.0.tar.gz>).

Can you please give me some guidance on this? I need the latest version, because of some bugs in version 2.3.0

Thank you,
Ioannis

--
Ioannis G. Riziotis
PhD Fellow
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

Re: [PyMOL] Assign different color to dash lines

[Ali K. <aku...@un...>]

Hi Mirna,

If you have generated a measure object like “measure01” i.e. using the measure wizard I PyMOL you can simply select the color like your would for any other PyMOL object. You can also use the set dash_color command to set all dashed lines to a single color, or selectively apply color to them i.e.
set dash_color, red, measure01

Cheers,

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
Supervised by A/Prof Thomas Balle
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050

From: Mirna Damergi <mir...@uc...>
Date: Thursday, 13 February 2020 at 8:27 am
To: "pym...@li..." <pym...@li...>
Subject: [PyMOL] Assign different color to dash lines

Good Afternoon,

I want to assign different colors to dash lines to highlight the distance of residues to atom A compared to atom B. Is that possible ?

Thank you,
Mirna
_________________________________
Mirna Damergi
BGSA VP Events
MSc Student, Noskov Lab
Centre of Molecular Simulation
Department of Biological Sciences
University of Calgary
mir...@uc...
LinkedIn: mirna-damergi<https://www.linkedin.com/in/mirna-damergi/>

[PyMOL] Assign different color to dash lines

[Mirna D. <mir...@uc...>]

Good Afternoon,

I want to assign different colors to dash lines to highlight the distance of residues to atom A compared to atom B. Is that possible ?

Thank you,
Mirna
_________________________________
Mirna Damergi
BGSA VP Events
MSc Student, Noskov Lab
Centre of Molecular Simulation
Department of Biological Sciences
University of Calgary
mir...@uc...
LinkedIn: mirna-damergi<https://www.linkedin.com/in/mirna-damergi/>

Re: [PyMOL] Open source v2.3.3

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

Hi Ioannis,

The corresponding commit was already pushed to master last May (
https://github.com/schrodinger/pymol-open-source/commit/6974848242f7685243c2ed648a957fa2cceb6de8).
Does is still not work?

On Wed, Feb 12, 2020 at 9:26 AM Ioannis Riziotis <riz...@eb...> wrote:

> Hello,
>
> I am using open-source pymol v2.3.0. However I have come across a bug when
> trying to ray trace transparent sticks, where transparency is not rendered
> at all. In a previous mail of mine, I was told that this issue had been
> fixed in version 2.3.3. This version is not available in GitHub to
> self-compile. Is there a way to obtain it?
>
> Regards,
> Ioannis
>
>
> --
> *Ioannis G. Riziotis*
> *PhD Fellow - Thornton Group*
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>

[PyMOL] Open source v2.3.3

[Ioannis R. <riz...@eb...>]

Hello,

I am using open-source pymol v2.3.0. However I have come across a bug when trying to ray trace transparent sticks, where transparency is not rendered at all. In a previous mail of mine, I was told that this issue had been fixed in version 2.3.3. This version is not available in GitHub to self-compile. Is there a way to obtain it? 

Regards,
Ioannis


--
Ioannis G. Riziotis
PhD Fellow - Thornton Group
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

[PyMOL] PyMOL crashes when building a nanotube

[Vyshnavi K. <ka...@hu...>]

Hi,

I'm building a nanotube by adding some polymer side chains to a nanotube
that I already have (pdb files). I've been able to do about 1/2 of adding
the side chains but now when I open the pse file or the saved project as a
pdb to continue editing it, PyMOL crashes as soon as I open the builder
tool. I get a pop up before the builder tool is loaded saying: "Building
"Undo" is disabled for the following objects
nanotube
Enable "Undo" for these objects? No/Yes"

I've tried both options (working after clicking "No" and after "Yes") and
PyMOL still crashes.

Any suggestions as to how to fix this? I have a grant proposal deadline
coming up and this novel molecule is the subject of that proposal.

Sincerely,
Vy
*Vyshnavi Karra (she/her/hers) *
*Ph.D Student, Northeastern University *
*M. Sc. Chemical Engineering, Rutgers University (2017) *
*B. S. Chemical Engineering, Rutgers University (2016) *

*Email: ka...@hu... <ka...@hu...> *

Re: [PyMOL] How to compile pymol with --glut?

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

Hi Yeping,

This has been asked before (by you :-)), see here:

https://sourceforge.net/p/pymol/mailman/message/36766620/

Cheers,
  Thomas

> On Feb 8, 2020, at 2:12 PM, 孙业平 via PyMOL-users <pym...@li...> wrote:
> 
> Dear pymol users,
> 
> I compiled pymol following the guide at https://pymolwiki.org/index.php/Linux_Install in my CentOS 8 system.
> When I tried to launch pymol by the "./pymol" command, I got the following error:
> 
>     Qt not available, using GLUT/Tk interface
> Traceback (most recent call last):
>   File "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", line 65, in <module>
>     pymol.launch(args)
>   File "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", line 441, in launch
>     _cmd.runpymol(_cmd._get_global_C_object(), block_input_hook)
> NotImplementedError: compile with --glut
> 
> I then removed the "bin" and the "lib64" directories in the "pymol-open-source-build" directory and recompiled pymol with the following command:
>        python3 setup --glut install --prefix=~/software/Pymol/pymol-open-source-build
> 
> However, the newly generated pymol binary file does not work either. Launch pymol give the same "Qt not available, using GLUT/Tk interface" error.
> 
> Could you help me with this?Thank you in advance.
> 
> Best regards.
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] floating external gui

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

Hi Tamas,

It is currently not possible to start PyMOL with a floating external GUI. The most convenient way to get it floating is to double click the empty space of the panel which toggles visibility of its title bar, then drag that out. See attached screenshot.




Cheers,
  Thomas

> On Feb 8, 2020, at 10:56 AM, Tamas Hegedus <bio...@gm...> wrote:
> 
> Hi,
> 
> I am using a compiled version of pymol.
> I like the floating window.
> 
> The CNTR-E does not work to toggle floating, I have to use the mouse (display, external gui, toggle floating).
> Is it possible to start pymol with floating external gui?
> 
> Thanks, Tamas
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Getting session file name

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

Hi Jason,

This should do it:

name = cmd.get('session_file')


Cheers,
  Thomas

> On Feb 8, 2020, at 5:21 AM, Junsu Park aka. Jason Mosier <par...@gm...> wrote:
> 
> Hello, this may be a very simple question that I just can't find the answer to, but I was wondering how I would go about fetching the session name of the .pse currently open? For example, I have two session files: colors and overlays, and I want my code to print something specific for each colors... and overlay... in a text file or whatever based on which one I have open
> 
> Cheers,
> Jason M.
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] How to compile pymol with --glut?

[<sun...@al...>]

Dear pymol users,

I compiled pymol following the guide at https://pymolwiki.org/index.php/Linux_Install in my CentOS 8 system.
When I tried to launch pymol by the "./pymol" command, I got the following error:

    Qt not available, using GLUT/Tk interface
Traceback (most recent call last):
  File "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", line 65, in <module>
    pymol.launch(args)
  File "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", line 441, in launch
    _cmd.runpymol(_cmd._get_global_C_object(), block_input_hook)
NotImplementedError: compile with --glut

I then removed the "bin" and the "lib64" directories in the "pymol-open-source-build" directory and recompiled pymol with the following command:
       python3 setup --glut install --prefix=~/software/Pymol/pymol-open-source-build

However, the newly generated pymol binary file does not work either. Launch pymol give the same "Qt not available, using GLUT/Tk interface" error.

Could you help me with this?Thank you in advance.

Best regards.

[PyMOL] floating external gui

[Tamas H. <bio...@gm...>]

Hi,

I am using a compiled version of pymol.
I like the floating window.

The CNTR-E does not work to toggle floating, I have to use the mouse (display, external gui, toggle floating).
Is it possible to start pymol with floating external gui?

Thanks, Tamas

[PyMOL] Getting session file name

[Junsu P. a. J. M. <par...@gm...>]

Hello, this may be a very simple question that I just can't find the answer
to, but I was wondering how I would go about fetching the session name of
the .pse currently open? For example, I have two session files: colors and
overlays, and I want my code to print something specific for each colors...
and overlay... in a text file or whatever based on which one I have open

Cheers,
Jason M.

[PyMOL] How to output the contact?

[<272...@qq...>]

Dear Pymol,


Manually clicking "(A)ction - find - any contact - between chains within 3.5A" can show the contacts. Can I ask


1) How can this commend be down using a script?


2) I would like to see the details of the contacts, e.g. which two residues/atoms are forming the contact. Is there a way to output a text file for all the contacts?


Thank you!


Yours sincerely
Cheng

[PyMOL] PyMol keeps crashing Help

[Victoria B. <vve...@uo...>]

Hi,

I have downloaded PyMol from my professors link (Version 1.7.4.5) and from
the website of PyMol (Version 2.3.4). My Macbook air is using MacOSCatalina
(Version 10.15.3). Everytime that I open it, it keeps crashing right away.
I have attached a transcript of the second window that opens up after the
app crashes. I would really appreciate some help with this issue, since I
need to use PyMol for my assignment.

Thank you,

Victoria V.

Process:               MacPyMOL [3196]
Path:                  /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL
Identifier:            com.schrodinger.macpymol
Version:               1.7.4.5 (1.7.4.5)
Code Type:             X86-64 (Native)
Parent Process:        ??? [1]
Responsible:           MacPyMOL [3196]
User ID:               501

Date/Time:             2020-02-04 13:22:09.806 -0500
OS Version:            Mac OS X 10.15.3 (19D76)
Report Version:        12
Anonymous UUID:        1E0D8DC1-7152-4233-7EC4-3087EFD5105C

Sleep/Wake UUID:       FE0C8F8B-68B5-4808-8B09-8DEFA2A93950

Time Awake Since Boot: 46000 seconds
Time Since Wake:       520 seconds

System Integrity Protection: enabled

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_INSTRUCTION (SIGILL)
Exception Codes:       0x0000000000000001, 0x0000000000000000
Exception Note:        EXC_CORPSE_NOTIFY

Termination Signal:    Illegal instruction: 4
Termination Reason:    Namespace SIGNAL, Code 0x4
Terminating Process:   exc handler [3196]

Application Specific Information:
*** CFRelease() called with NULL ***

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   com.apple.CoreFoundation       0x00007fff30407cde CFRelease.cold.1 + 14
1   com.apple.CoreFoundation       0x00007fff302611f2 CFRelease + 101
2   com.schrodinger.macpymol       0x000000010a8cf46c -[PMG_Aqua idle] + 796
3   com.schrodinger.macpymol       0x000000010a8d7077 __35-[PyMOLOpenGLView
getFrameForTime:]_block_invoke + 535
4   libdispatch.dylib              0x00007fff6778b583
_dispatch_call_block_and_release + 12
5   libdispatch.dylib              0x00007fff6778c50e
_dispatch_client_callout + 8
6   libdispatch.dylib              0x00007fff67797bc4
_dispatch_main_queue_callback_4CF + 1105
7   com.apple.CoreFoundation       0x00007fff30319e00
__CFRUNLOOP_IS_SERVICING_THE_MAIN_DISPATCH_QUEUE__ + 9
8   com.apple.CoreFoundation       0x00007fff302d9b8a __CFRunLoopRun + 2370
9   com.apple.CoreFoundation       0x00007fff302d8bd3 CFRunLoopRunSpecific
+ 499
10  com.apple.HIToolbox            0x00007fff2ee2e65d
RunCurrentEventLoopInMode + 292
11  com.apple.HIToolbox            0x00007fff2ee2e39d
ReceiveNextEventCommon + 600
12  com.apple.HIToolbox            0x00007fff2ee2e127
_BlockUntilNextEventMatchingListInModeWithFilter + 64
13  com.apple.AppKit               0x00007fff2d49eba4 _DPSNextEvent + 990
14  com.apple.AppKit               0x00007fff2d49d380
-[NSApplication(NSEvent)
_nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
15  com.apple.AppKit               0x00007fff2d48f09e -[NSApplication run]
+ 658
16  com.schrodinger.macpymol       0x000000010a8dad98 main + 5480
17  com.schrodinger.macpymol       0x000000010a5c1b64 start + 52

Thread 1:
0   libsystem_pthread.dylib        0x00007fff679e5818 start_wqthread + 0

Thread 2:
0   libsystem_pthread.dylib        0x00007fff679e5818 start_wqthread + 0

Thread 3:
0   libsystem_pthread.dylib        0x00007fff679e5818 start_wqthread + 0

Thread 4:
0   libsystem_pthread.dylib        0x00007fff679e5818 start_wqthread + 0

Thread 5:: CVDisplayLink
0   libsystem_kernel.dylib         0x00007fff67928ce6 __psynch_cvwait + 10
1   libsystem_pthread.dylib        0x00007fff679ea1b7 _pthread_cond_wait +
751
2   com.apple.CoreVideo            0x00007fff32273bab
CVDisplayLink::waitUntil(unsigned long long) + 229
3   com.apple.CoreVideo            0x00007fff322730b8
CVDisplayLink::runIOThread() + 482
4   libsystem_pthread.dylib        0x00007fff679e9e65 _pthread_start + 148
5   libsystem_pthread.dylib        0x00007fff679e583b thread_start + 15

Thread 6:: CVDisplayLink
0   libsystem_kernel.dylib         0x00007fff67928ce6 __psynch_cvwait + 10
1   libsystem_pthread.dylib        0x00007fff679ea1b7 _pthread_cond_wait +
751
2   com.apple.CoreVideo            0x00007fff32273bab
CVDisplayLink::waitUntil(unsigned long long) + 229
3   com.apple.CoreVideo            0x00007fff322730b8
CVDisplayLink::runIOThread() + 482
4   libsystem_pthread.dylib        0x00007fff679e9e65 _pthread_start + 148
5   libsystem_pthread.dylib        0x00007fff679e583b thread_start + 15

Thread 7:: CVDisplayLink
0   libsystem_kernel.dylib         0x00007fff67928ce6 __psynch_cvwait + 10
1   libsystem_pthread.dylib        0x00007fff679ea1b7 _pthread_cond_wait +
751
2   com.apple.CoreVideo            0x00007fff32273bab
CVDisplayLink::waitUntil(unsigned long long) + 229
3   com.apple.CoreVideo            0x00007fff322730b8
CVDisplayLink::runIOThread() + 482
4   libsystem_pthread.dylib        0x00007fff679e9e65 _pthread_start + 148
5   libsystem_pthread.dylib        0x00007fff679e583b thread_start + 15

Thread 8:: com.apple.NSEventThread
0   libsystem_kernel.dylib         0x00007fff6792625a mach_msg_trap + 10
1   libsystem_kernel.dylib         0x00007fff679265d0 mach_msg + 60
2   com.apple.CoreFoundation       0x00007fff302dad0b
__CFRunLoopServiceMachPort + 322
3   com.apple.CoreFoundation       0x00007fff302d98e7 __CFRunLoopRun + 1695
4   com.apple.CoreFoundation       0x00007fff302d8bd3 CFRunLoopRunSpecific
+ 499
5   com.apple.AppKit               0x00007fff2d641792 _NSEventThread + 132
6   libsystem_pthread.dylib        0x00007fff679e9e65 _pthread_start + 148
7   libsystem_pthread.dylib        0x00007fff679e583b thread_start + 15

Thread 9:
0   libsystem_kernel.dylib         0x00007fff67927916 __getdirentries64 + 10
1   libsystem_c.dylib              0x00007fff6785dc05
_readdir_unlocked$INODE64 + 201
2   libsystem_c.dylib              0x00007fff6785dcd5 readdir$INODE64 + 35
3   org.python.python              0x00007fff3b21c54a 0x7fff3b182000 +
632138
4   org.python.python              0x00007fff3b21adf4 0x7fff3b182000 +
626164
5   org.python.python              0x00007fff3b21cac4 0x7fff3b182000 +
633540
6   org.python.python              0x00007fff3b21c6d7 0x7fff3b182000 +
632535
7   org.python.python              0x00007fff3b21b6d6
PyImport_ImportModuleLevel + 582
8   org.python.python              0x00007fff3b1fe8c0 0x7fff3b182000 +
510144
9   org.python.python              0x00007fff3b18c319 PyObject_Call + 97
10  org.python.python              0x00007fff3b20c3d9
PyEval_CallObjectWithKeywords + 159
11  org.python.python              0x00007fff3b207164 PyEval_EvalFrameEx +
15862
12  org.python.python              0x00007fff3b202d5e PyEval_EvalCodeEx +
534
13  org.python.python              0x00007fff3b202b42 PyEval_EvalCode + 32
14  org.python.python              0x00007fff3b21a2ae
PyImport_ExecCodeModuleEx + 212
15  org.python.python              0x00007fff3b21d033 0x7fff3b182000 +
634931
16  org.python.python              0x00007fff3b21caff 0x7fff3b182000 +
633599
17  org.python.python              0x00007fff3b21c6d7 0x7fff3b182000 +
632535
18  org.python.python              0x00007fff3b21b6d6
PyImport_ImportModuleLevel + 582
19  org.python.python              0x00007fff3b1fe8c0 0x7fff3b182000 +
510144
20  org.python.python              0x00007fff3b18c319 PyObject_Call + 97
21  org.python.python              0x00007fff3b20c3d9
PyEval_CallObjectWithKeywords + 159
22  org.python.python              0x00007fff3b207164 PyEval_EvalFrameEx +
15862
23  org.python.python              0x00007fff3b202d5e PyEval_EvalCodeEx +
534
24  org.python.python              0x00007fff3b202b42 PyEval_EvalCode + 32
25  org.python.python              0x00007fff3b21a2ae
PyImport_ExecCodeModuleEx + 212
26  org.python.python              0x00007fff3b21d033 0x7fff3b182000 +
634931
27  org.python.python              0x00007fff3b21caff 0x7fff3b182000 +
633599
28  org.python.python              0x00007fff3b21c724 0x7fff3b182000 +
632612
29  org.python.python              0x00007fff3b21b6d6
PyImport_ImportModuleLevel + 582
30  org.python.python              0x00007fff3b1fe8c0 0x7fff3b182000 +
510144
31  org.python.python              0x00007fff3b18c319 PyObject_Call + 97
32  org.python.python              0x00007fff3b20c3d9
PyEval_CallObjectWithKeywords + 159
33  org.python.python              0x00007fff3b207164 PyEval_EvalFrameEx +
15862
34  org.python.python              0x00007fff3b202d5e PyEval_EvalCodeEx +
534
35  org.python.python              0x00007fff3b1a9c85 0x7fff3b182000 +
162949
36  org.python.python              0x00007fff3b18c319 PyObject_Call + 97
37  org.python.python              0x00007fff3b208c30 PyEval_EvalFrameEx +
22722
38  org.python.python              0x00007fff3b20ca37 0x7fff3b182000 +
567863
39  org.python.python              0x00007fff3b2082c2 PyEval_EvalFrameEx +
20308
40  org.python.python              0x00007fff3b20ca37 0x7fff3b182000 +
567863
41  org.python.python              0x00007fff3b2082c2 PyEval_EvalFrameEx +
20308
42  org.python.python              0x00007fff3b202d5e PyEval_EvalCodeEx +
534
43  org.python.python              0x00007fff3b1a9c85 0x7fff3b182000 +
162949
44  org.python.python              0x00007fff3b18c319 PyObject_Call + 97
45  org.python.python              0x00007fff3b196afe 0x7fff3b182000 + 84734
46  org.python.python              0x00007fff3b18c319 PyObject_Call + 97
47  org.python.python              0x00007fff3b20c3d9
PyEval_CallObjectWithKeywords + 159
48  org.python.python              0x00007fff3b238780 0x7fff3b182000 +
747392
49  org.python.python              0x00007fff3b234463 0x7fff3b182000 +
730211
50  libsystem_pthread.dylib        0x00007fff679e9e65 _pthread_start + 148
51  libsystem_pthread.dylib        0x00007fff679e583b thread_start + 15

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x00007fff305f17ee  rbx: 0x0000600000255dc0  rcx: 0x0000000100000000
 rdx: 0x000000010bed3000
  rdi: 0x0000000000000000  rsi: 0x00007fff717fffe8  rbp: 0x00007ffee5643120
 rsp: 0x00007ffee5643118
   r8: 0x000000010000163e   r9: 0x0000000000000000  r10: 0x00007ffee5645cd8
 r11: 0x00007fff3026118d
  r12: 0x00007fbe2d630de0  r13: 0x0000000000000004  r14: 0x0000000000000001
 r15: 0x0000000000000000
  rip: 0x00007fff30407cde  rfl: 0x0000000000010246  cr2: 0x00000001121f007d

Logical CPU:     1
Error Code:      0x00000000
Trap Number:     6


Binary Images:
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