pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] molmol to pymol

[Yanan He <he...@um...>]

Hi All,

How can I convert MOLMOL format coordinates to PYMOL format? The reason for
me to do this is because I need to deposit my MOLMOL aligned NMR ensemble
to PDB, but it is  not recognized by PDB for the format difference.

Any help will be very helpful, thanks.

Yanan

Re: [PyMOL] PyMOL 2.5 released

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

Hi,

Open-source features are typically added on a rolling basis as they're
implemented (for example, support for curved helices have been in open
source since last October), so many of the features listed here (the
non-Incentive Only ones) should have already applied. If they aren't, feel
free to open a ticket on the open-source github repo. A PyMOL 2.5 github
tag and source release archive should also be uploaded within the next hour
or so.

Best,

Jarrett J

On Mon, May 10, 2021 at 1:59 PM Stephen P. Molnar <s.m...@sb...>
wrote:

> very good.
>
> When will this migrate to github.com/schrodinger/pymol-open-source.git?
>
> On 05/10/2021 12:27 PM, Jarrett Johnson wrote:
>
> Greetings,
>
> We are happy to announce the release of PyMOL 2.5. Download ready-to-use
> bundles from https://pymol.org/ or update your installation with "conda
> install -c schrodinger pymol".
>
> New features include:
> - Multiple-level undo for PyMOL actions (Incentive Only)
> - Curved cartoon cylindrical helices
> - Customizable keyboard shortcut menu
> - Improved isosurface generation
> - Nucleotides from the PDB can now be extended in builder (Incentive Only)
> - Improved MAE import (Incentive Only)
> - ...and more. Please check our release notes.
>
> Python 2 support has been removed. Python 2 to 3 converter tools including
> 2to3 may be useful if you need to update python scripts.
>
> Find the complete release notes at:
> https://pymol.org/d/media:new25
>
> We welcome any feedback and bug reports.
>
> Cheers,
> - The PyMOL Team at Schr�dinger
>
> --
>
> *Jarrett Johnson*�| Senior Developer
> [image: Schrodinger Logo] <https://www.schrodinger.com/>
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
> --
> Stephen P. Molnar, Ph.D.www.molecular-modeling.net
> 614.312.7528 (c)
> Skype:  smolnar1
>
>
> _______________________________________________
> 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/>

Re: [PyMOL] PyMOL 2.5 released

[Stephen P. M. <s.m...@sb...>]

very good.

When will this migrate to github.com/schrodinger/pymol-open-source.git?

On 05/10/2021 12:27 PM, Jarrett Johnson wrote:
> Greetings,
>
> We are happy to announce the release of PyMOL 2.5. Download 
> ready-to-use bundles from https://pymol.org/ or update your 
> installation with "conda install -c schrodinger pymol".
>
> New features include:
> - Multiple-level undo for PyMOL actions (Incentive Only)
> - Curved cartoon cylindrical helices
> - Customizable keyboard shortcut menu
> - Improved isosurface generation
> - Nucleotides from the PDB can now be extended in builder (Incentive Only)
> - Improved MAE import (Incentive Only)
> - ...and more. Please check our release notes.
>
> Python 2 support has been removed. Python 2 to 3 converter tools 
> including 2to3 may be useful if you need to update python scripts.
>
> Find the complete release notes at:
> https://pymol.org/d/media:new25
>
> We welcome any feedback and bug reports.
>
> Cheers,
> - The PyMOL Team at Schr�dinger
>
> -- 
>
> *Jarrett Johnson* | Senior Developer
>
> Schrodinger Logo <https://www.schrodinger.com/>
>
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

-- 
Stephen P. Molnar, Ph.D.
www.molecular-modeling.net
614.312.7528 (c)
Skype:  smolnar1

[PyMOL] PyMOL 2.5 released

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

Greetings,

We are happy to announce the release of PyMOL 2.5. Download ready-to-use
bundles from https://pymol.org/ or update your installation with "conda
install -c schrodinger pymol".

New features include:
- Multiple-level undo for PyMOL actions (Incentive Only)
- Curved cartoon cylindrical helices
- Customizable keyboard shortcut menu
- Improved isosurface generation
- Nucleotides from the PDB can now be extended in builder (Incentive Only)
- Improved MAE import (Incentive Only)
- ...and more. Please check our release notes.

Python 2 support has been removed. Python 2 to 3 converter tools including
2to3 may be useful if you need to update python scripts.

Find the complete release notes at:
https://pymol.org/d/media:new25

We welcome any feedback and bug reports.

Cheers,
- The PyMOL Team at Schrödinger

-- 

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

Re: [PyMOL] Cartoon_transparency

[Criss H. <cri...@gm...>]

Transparency mode solves it. Thanks.

On Sat, May 8, 2021 at 2:41 PM Jarrett Johnson <
jar...@sc...> wrote:

> Hi Criss,
>
> It doesn't appear to be broken from what I see. Helices may not appear
> transparent to each other if you're using single-layer transparency by
> default. Setting `transparency_mode` to 3 should show transparent objects
> beneath each other.
>
> https://pymolwiki.org/index.php/Transparency_mode
>
> Best,
>
> Jarrett J
>
> On Sat, May 8, 2021 at 10:01 AM Criss Hartzell <cri...@gm...>
> wrote:
>
>> I am using PYMOL2.4.1 on windows.
>> I want to make two cartoon helices transparent in an object having 10
>> heleices. Before version 2.3, I would make a copy of the object, hide the
>> two transparent helices on the original object and show them on the copy
>> with transparency set to 0.5. After PYMOL2.3, cartoon-transparency is
>> supposed to work on the atom level, but when I try to apply cartoon
>> transparency to the two helices as a selection
>> (cartoon_transparency,0.5,sele), the helices change color but do not become
>> transparent. Am I doing something wrong?
>>
>> --
>> Criss Hartzell
>> _______________________________________________
>> 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/>
>


-- 
Criss Hartzell

Re: [PyMOL] Cartoon_transparency

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

Hi Criss,

It doesn't appear to be broken from what I see. Helices may not appear
transparent to each other if you're using single-layer transparency by
default. Setting `transparency_mode` to 3 should show transparent objects
beneath each other.

https://pymolwiki.org/index.php/Transparency_mode

Best,

Jarrett J

On Sat, May 8, 2021 at 10:01 AM Criss Hartzell <cri...@gm...>
wrote:

> I am using PYMOL2.4.1 on windows.
> I want to make two cartoon helices transparent in an object having 10
> heleices. Before version 2.3, I would make a copy of the object, hide the
> two transparent helices on the original object and show them on the copy
> with transparency set to 0.5. After PYMOL2.3, cartoon-transparency is
> supposed to work on the atom level, but when I try to apply cartoon
> transparency to the two helices as a selection
> (cartoon_transparency,0.5,sele), the helices change color but do not become
> transparent. Am I doing something wrong?
>
> --
> Criss Hartzell
> _______________________________________________
> 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] Cartoon_transparency

[Criss H. <cri...@gm...>]

I am using PYMOL2.4.1 on windows.
I want to make two cartoon helices transparent in an object having 10
heleices. Before version 2.3, I would make a copy of the object, hide the
two transparent helices on the original object and show them on the copy
with transparency set to 0.5. After PYMOL2.3, cartoon-transparency is
supposed to work on the atom level, but when I try to apply cartoon
transparency to the two helices as a selection
(cartoon_transparency,0.5,sele), the helices change color but do not become
transparent. Am I doing something wrong?

-- 
Criss Hartzell

Re: [PyMOL] Pymol in conda-forge osx-arm64 for new M1 Macs

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

Hi Florian,

This is an eventual goal for the *schrodinger *channel. First I'd like to
have conda-forge's qt/pyqt support osx-arm64 and our CI runner which
provides the mac builds support M1 too.

Best,

Jarrett J.

On Mon, May 3, 2021 at 11:34 AM Florian Nachon <mai...@na...>
wrote:

> Hello,
>
> I want to install a native version of Pymol for the new M1 Mac with conda
> but Pymol is not yet in the new osx-arm64 platform in conda-forge (
> https://conda-forge.org/blog/posts/2020-10-29-macos-arm64/)
>
> Is there any work to put it there?
>
> What about an arm64 version in Schrodinger's channel? (
> https://anaconda.org/schrodinger)
>
> Thanx for any clues!
>
> Florian
> _______________________________________________
> 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/>

Re: [PyMOL] Scroll wheel not slabbing

[Marko H. <mh...@ca...>]

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  </head>
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    <font face="monospace">Thanks - that fixed it!<br>
      <br>
      best, Marko<br>
    </font><br>
    <div class="moz-cite-prefix">On 02/05/2021 19:56, Christoph Gohlke
      wrote:<br>
    </div>
    <blockquote type="cite"
      cite="mid:217...@uc...">Regarding
      Pmw: pip uninstall Pmw and install Pmw-2.0.1-py3-none-any.whl from
<a class="moz-txt-link-rfc2396E" href="https://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol-open-source">&lt;https://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol-open-source&gt;</a>
      <br>
      <br>
      Christoph
      <br>
      <br>
      <br>
      On 5/2/2021 11:43 AM, Marko Hyvonen wrote:
      <br>
      <blockquote type="cite">Hello PyMOLers
        <br>
        <br>
        Just installed open source 2.4 with Python 3.9 and all seems ok
        apart from the mouse scroll wheel not doing anything when I move
        PyMOL to the external screen of my laptop,  ie. I get no
        slabbing in viewing mode. Moving PyMOL back to the laptop screen
        restores scrolling and it seems to happen only when I used
        extended desktop - duplicate screen or external only work fine.
        Any idea what could be the issue? A bit of a pain as I prefer
        the external screen for mol graphics.
        <br>
        <br>
        My old version 1.8.2 works correctly.
        <br>
        <br>
        Also Plugin manager does seem to work. Seem to get a lot of
        errors related to Pmw (which is up to date). Any ideas? Errors
        below.
        <br>
        <br>
        cheers, Marko
        <br>
        <br>
        <br>
        TypeError Exception in Tk callback
        <br>
           Function: &lt;function
        addPluginManagerMenuItem.&lt;locals&gt;.plugin_manager at
        0x00000234B6DCDCA0&gt; (type: &lt;class 'function'&gt;)
        <br>
           Args: ()
        <br>
        Traceback (innermost last):
        <br>
           File
        "C:\Python39\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwBase.py",
        line 1776, in __call__
        <br>
             return self.func(*args)
        <br>
           File
        "C:\Python39\lib\site-packages\pymol\plugins\legacysupport.py",
        line 87, in plugin_manager
        <br>
             managergui.manager_dialog()
        <br>
           File
        "C:\Python39\lib\site-packages\pymol\plugins\managergui.py",
        line 47, in manager_dialog
        <br>
             dialog = PluginManager(get_tk_root())
        <br>
           File
        "C:\Python39\lib\site-packages\pymol\plugins\managergui.py",
        line 129, in __init__
        <br>
             notebook = Pmw.NoteBook(master)
        <br>
           File
        "C:\Python39\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwNoteBook.py",
        line 60, in __init__
        <br>
             Pmw.Color.bordercolors(self, self['hull_background'])
        <br>
           File
        "C:\Python39\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwColor.py",
        line 359, in bordercolors
        <br>
             '#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),
        <br>
        TypeError: %x format: an integer is required, not float
        <br>
        <br>
        -- <br>
        <br>
        Marko Hyvonen
        <br>
        Department of Biochemistry, University of Cambridge
        <br>
        <a class="moz-txt-link-abbreviated" href="mailto:mh...@ca...">mh...@ca...</a>
        <br>
        +44 (0)1223 766 044
        <br>
        @HyvonenGroup
        <br>
        <a class="moz-txt-link-freetext" href="http://hyvonen.bioc.cam.ac.uk">http://hyvonen.bioc.cam.ac.uk</a>
        <br>
          <br>
        <br>
        <br>
        _______________________________________________
        <br>
        PyMOL-users mailing list
        <br>
        Archives:
        <a class="moz-txt-link-freetext" href="http://www.mail-archive.com/pym...@li...">http://www.mail-archive.com/pym...@li...</a>
        <br>
        Unsubscribe:
        <a class="moz-txt-link-freetext" href="https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe">https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe</a>
        <br>
        <br>
      </blockquote>
      <br>
      <br>
      _______________________________________________
      <br>
      PyMOL-users mailing list
      <br>
      Archives:
      <a class="moz-txt-link-freetext" href="http://www.mail-archive.com/pym...@li...">http://www.mail-archive.com/pym...@li...</a>
      <br>
      Unsubscribe:
      <a class="moz-txt-link-freetext" href="https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe">https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe</a><br>
    </blockquote>
    <br>
    <pre class="moz-signature" cols="72">-- 

Marko Hyvonen
Department of Biochemistry, University of Cambridge
<a class="moz-txt-link-abbreviated" href="mailto:mh...@ca...">mh...@ca...</a>
+44 (0)1223 766 044
@HyvonenGroup
<a class="moz-txt-link-freetext" href="http://hyvonen.bioc.cam.ac.uk">http://hyvonen.bioc.cam.ac.uk</a>
 

</pre>
  </body>
</html>

[PyMOL] Pymol in conda-forge osx-arm64 for new M1 Macs

[Florian N. <mai...@na...>]

Hello,

I want to install a native version of Pymol for the new M1 Mac with conda but Pymol is not yet in the new osx-arm64 platform in conda-forge (https://conda-forge.org/blog/posts/2020-10-29-macos-arm64/ <https://conda-forge.org/blog/posts/2020-10-29-macos-arm64/>)

Is there any work to put it there?

What about an arm64 version in Schrodinger's channel? (https://anaconda.org/schrodinger <https://anaconda.org/schrodinger>)

Thanx for any clues!

Florian

Re: [PyMOL] Scroll wheel not slabbing

[Christoph G. <cg...@uc...>]

Regarding Pmw: pip uninstall Pmw and install Pmw-2.0.1-py3-none-any.whl 
from <https://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol-open-source>

Christoph


On 5/2/2021 11:43 AM, Marko Hyvonen wrote:
> Hello PyMOLers
> 
> Just installed open source 2.4 with Python 3.9 and all seems ok apart 
> from the mouse scroll wheel not doing anything when I move PyMOL to the 
> external screen of my laptop,  ie. I get no slabbing in viewing mode. 
> Moving PyMOL back to the laptop screen restores scrolling and it seems 
> to happen only when I used extended desktop - duplicate screen or 
> external only work fine. Any idea what could be the issue? A bit of a 
> pain as I prefer the external screen for mol graphics.
> 
> My old version 1.8.2 works correctly.
> 
> Also Plugin manager does seem to work. Seem to get a lot of errors 
> related to Pmw (which is up to date). Any ideas? Errors below.
> 
> cheers, Marko
> 
> 
> TypeError Exception in Tk callback
>    Function: <function addPluginManagerMenuItem.<locals>.plugin_manager 
> at 0x00000234B6DCDCA0> (type: <class 'function'>)
>    Args: ()
> Traceback (innermost last):
>    File "C:\Python39\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwBase.py", 
> line 1776, in __call__
>      return self.func(*args)
>    File "C:\Python39\lib\site-packages\pymol\plugins\legacysupport.py", 
> line 87, in plugin_manager
>      managergui.manager_dialog()
>    File "C:\Python39\lib\site-packages\pymol\plugins\managergui.py", 
> line 47, in manager_dialog
>      dialog = PluginManager(get_tk_root())
>    File "C:\Python39\lib\site-packages\pymol\plugins\managergui.py", 
> line 129, in __init__
>      notebook = Pmw.NoteBook(master)
>    File 
> "C:\Python39\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwNoteBook.py", line 
> 60, in __init__
>      Pmw.Color.bordercolors(self, self['hull_background'])
>    File "C:\Python39\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwColor.py", 
> line 359, in bordercolors
>      '#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),
> TypeError: %x format: an integer is required, not float
> 
> -- 
> 
> Marko Hyvonen
> Department of Biochemistry, University of Cambridge
> mh...@ca...
> +44 (0)1223 766 044
> @HyvonenGroup
> http://hyvonen.bioc.cam.ac.uk
>   
> 
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 

[PyMOL] Scroll wheel not slabbing

[Marko H. <mh...@ca...>]

<html>
  <head>

    <meta http-equiv="content-type" content="text/html; charset=UTF-8">
  </head>
  <body>
    <font face="monospace">Hello PyMOLers<br>
      <br>
      Just installed open source 2.4 with Python 3.9 and all seems ok
      apart from the mouse scroll wheel not doing anything when I move
      PyMOL to the external screen of my laptop,  ie. I get no slabbing
      in viewing mode. Moving PyMOL back to the laptop screen restores
      scrolling and it seems to happen only when I used extended desktop
      - duplicate screen or external only work fine. Any idea what could
      be the issue? A bit of a pain as I prefer the external screen for
      mol graphics. <br>
      <br>
      My old version 1.8.2 works correctly. <br>
      <br>
      Also Plugin manager does seem to work. Seem to get a lot of errors
      related to Pmw (which is up to date). Any ideas? Errors below. <br>
      <br>
      cheers, Marko<br>
      <br>
      <br>
      TypeError Exception in Tk callback<br>
        Function: &lt;function
      addPluginManagerMenuItem.&lt;locals&gt;.plugin_manager at
      0x00000234B6DCDCA0&gt; (type: &lt;class 'function'&gt;)<br>
        Args: ()<br>
      Traceback (innermost last):<br>
        File
      "C:\Python39\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwBase.py", line
      1776, in __call__<br>
          return self.func(*args)<br>
        File
      "C:\Python39\lib\site-packages\pymol\plugins\legacysupport.py",
      line 87, in plugin_manager<br>
          managergui.manager_dialog()<br>
        File
      "C:\Python39\lib\site-packages\pymol\plugins\managergui.py", line
      47, in manager_dialog<br>
          dialog = PluginManager(get_tk_root())<br>
        File
      "C:\Python39\lib\site-packages\pymol\plugins\managergui.py", line
      129, in __init__<br>
          notebook = Pmw.NoteBook(master)<br>
        File
      "C:\Python39\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwNoteBook.py",
      line 60, in __init__<br>
          Pmw.Color.bordercolors(self, self['hull_background'])<br>
        File
      "C:\Python39\lib\site-packages\Pmw\Pmw_2_0_1\lib\PmwColor.py",
      line 359, in bordercolors<br>
          '#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),<br>
      TypeError: %x format: an integer is required, not float<br>
    </font>
    <pre class="moz-signature" cols="72">-- 

Marko Hyvonen
Department of Biochemistry, University of Cambridge
<a class="moz-txt-link-abbreviated" href="mailto:mh...@ca...">mh...@ca...</a>
+44 (0)1223 766 044
@HyvonenGroup
<a class="moz-txt-link-freetext" href="http://hyvonen.bioc.cam.ac.uk">http://hyvonen.bioc.cam.ac.uk</a>
 

</pre>
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</html>

Re: [PyMOL] Farewell

[Jason K. <ke...@hk...>]

Hi Everyone,

I'd like to publicly thank Thomas for his contribution to PyMOL over
the last decade.

PyMOL is the primary tool the broader scientific community uses to
access the results we create as structural biologists.
For many researchers, PyMOL is their first window into macromolecular
structures. And, at the very least, journal covers are MUCH nicer
because of it.
It is, without doubt, the most popular title in the SBGrid
installation. It always has been.

I assure everyone here that creating reliable software that runs on 3
operating systems with an open source model and great user support is
no easy task.
Sustaining that effort for nearly 10 years is another feat altogether.

If you'd like to see how far PyMOL has come, here's a webinar we did
(live!) in 2013 here :
https://www.youtube.com/watch?v=UHOUFJmj_fM

Best of luck in your next chapter Thomas!

Cheers,
Jason

-- 
Jason Key, PhD
Project Lead
SBGrid Consortium, Harvard Medical School

Re: [PyMOL] Farewell

[David G. <dd...@uc...>]

Dear Thomas Holder, 

Thank you for helping out PyMOL users like myself. Also putting up user friendly advise for the over the years who use PyMOL. 
I tend to read your email correspondence with other users, since they seem to be more thought through than my few emails I asked in these forums. 
I hope a lot more experts can do the same for people who are teaching molecular modeling or learning PyMOL. 

Sincerely,
David Gae

> On Apr 30, 2021, at 7:14 AM, Thomas Holder <tho...@sc...> wrote:
> 
> Dear PyMOL community -
> 
> The time has come for me to hand over my PyMOL development
> responsibilities at Schrödinger. It's been an incredible journey for
> me to get involved with the PyMOL community, to become a PyMOL fellow
> in 2011 and to start working full time for the project in 2012. I'm
> extremely grateful to all the people at Schrödinger who made this
> possible, and of course to all of you - the user community - who've
> shown me every day that my work is meaningful.
> 
> PyMOL has a unique place within Schrödinger, and a highly motivated
> and skilled team of developers and scientists stand behind it. They
> have some great plans and I'm excited to watch how they will take
> PyMOL to the next level.
> 
> I don't think that my PyMOL journey is over yet. But for the next
> chapter in my career, I'll "just" be a user and a member of the
> community. See you around.
> 
> Cheers,
>  Thomas
> 
> -- 
> 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

Re: [PyMOL] Farewell

[H. A. S. <h.a...@gm...>]

Thank you Thomas for all the help you have provided us over the years! You have certainly made my experience with PyMOL far more useful and easier, with all of the answers and shortcuts you have provided to this list!

Adam


> On Apr 30, 2021, at 9:14 AM, Thomas Holder <tho...@sc...> wrote:
> 
> Dear PyMOL community -
> 
> The time has come for me to hand over my PyMOL development
> responsibilities at Schrödinger. It's been an incredible journey for
> me to get involved with the PyMOL community, to become a PyMOL fellow
> in 2011 and to start working full time for the project in 2012. I'm
> extremely grateful to all the people at Schrödinger who made this
> possible, and of course to all of you - the user community - who've
> shown me every day that my work is meaningful.
> 
> PyMOL has a unique place within Schrödinger, and a highly motivated
> and skilled team of developers and scientists stand behind it. They
> have some great plans and I'm excited to watch how they will take
> PyMOL to the next level.
> 
> I don't think that my PyMOL journey is over yet. But for the next
> chapter in my career, I'll "just" be a user and a member of the
> community. See you around.
> 
> Cheers,
>  Thomas
> 
> -- 
> 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] Farewell

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

Dear PyMOL community -

The time has come for me to hand over my PyMOL development
responsibilities at Schrödinger. It's been an incredible journey for
me to get involved with the PyMOL community, to become a PyMOL fellow
in 2011 and to start working full time for the project in 2012. I'm
extremely grateful to all the people at Schrödinger who made this
possible, and of course to all of you - the user community - who've
shown me every day that my work is meaningful.

PyMOL has a unique place within Schrödinger, and a highly motivated
and skilled team of developers and scientists stand behind it. They
have some great plans and I'm excited to watch how they will take
PyMOL to the next level.

I don't think that my PyMOL journey is over yet. But for the next
chapter in my career, I'll "just" be a user and a member of the
community. See you around.

Cheers,
  Thomas

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Custom selection operators

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

Hi Ioannis,

Might need more information regarding what you mean about 'complex
property', but if you want a selection to include descriptors A, B, and C
into a selection, something like

```
select your_sele, (A | B | C)
```
would suffice.

or
```
select your_sele, A
select your_sele, (your_sele | B)
select your_sele, (your_sele | C)
```

Hope that helps,

Jarrett J

On Wed, Apr 14, 2021 at 8:03 AM Ioannis Riziotis <riz...@eb...> wrote:

> Hello,
>
> Is there any way to define a custom selection operator in a script? E.g.
> select all atoms with complex properties A, B, and C.
>
> Otherwise, what is the proper way of appending atoms to a selection in
> scripting?
>
> Thank you,
> Yannis
>
>
>
> _______________________________________________
> 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/>

Re: [PyMOL] Running PyMOL on a headless machine

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

Hi Andras,

Thanks for reporting this issue and for posting your solution/workaround.
This issue will be fixed in PyMOL 2.5.

Cheers,
  Thomas

On Wed, Mar 24, 2021 at 10:25 AM András Ferenc WACHA
<wac...@tt...> wrote:
>
> Dear fellow PyMOL users,
>
> I have found a solution (at least a workaround):
>
> pymol -cpihq <<EOF
>
> import pymol.plugins
>
> pymol.plugins.initialize(-1)
>
> ...
>
> EOF
>
> This way all plug-ins are loaded in the same way as when graphics mode is used, but the legacy Tk-based app part (which threw the exception) is not initialized.
>
> Kind regards,
>
> Andras
>
> On 3/24/21 9:48 AM, András Ferenc WACHA wrote:
>
> Dear fellow PyMOL users,
>
> I'm trying to run open source PyMOL v2.4.0 on a Linux computer with no X11 available (as part of a script on a HPC cluster). I noticed that plug-ins are not loaded automatically, therefore I force the required plug-in (pmlbeta) to load as follows:
>
> pymol -cpihq <<EOF
>
> import pymol.plugins
>
> pymol.plugins.plugin_load('pmlbeta')  # or "apbs_tools" or "lightingsettings_gui"
>
> EOF
>
> However, an exception is thrown by PyMOL:
>
> Exception in thread Thread-2:
> Traceback (most recent call last):
>   File "/opt/miniconda3/envs/gmxbatch/lib/python3.9/threading.py", line 954, in _bootstrap_inner
>     self.run()
>   File "/opt/miniconda3/envs/gmxbatch/lib/python3.9/threading.py", line 892, in run
>     self._target(*self._args, **self._kwargs)
>   File "/opt/miniconda3/envs/gmxbatch/lib/python3.9/site-packages/pymol/plugins/legacysupport.py", line 134, in starttk
>     app.root = Tkinter.Tk()
>   File "/opt/miniconda3/envs/gmxbatch/lib/python3.9/tkinter/__init__.py", line 2270, in __init__
>     self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
> _tkinter.TclError: no display name and no $DISPLAY environment variable
>
> I have ascertained that the exception occurs even before the __init__.py module of my plugin starts running.
>
> In principle, my plug-in does not strictly need graphics, I would like to use only the custom commands supplied by my plug-in (e.g. with cmd.extend()).
>
> Is this possible? Or do I do something wrong (e.g. the forced loading of the plug-in)?
>
> Kind regards,
>
> Andras Wacha
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> --
> András Ferenc Wacha, PhD
> research fellow, CREDO instrument responsible
>
> Biological Nanochemistry Research Group (310)
>
> Institute of Materials and Environmental Chemistry
> Research Centre for Natural Sciences (RCNS)
> Magyar tudósok körútja 2.
> H-1117 Budapest, Hungary
> Phone: +36-1-382-6427
> Web: http://bionano.ttk.hu
> CREDO SAXS instrument: http://credo.ttk.hu
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Problem with Pymol following update to Mac Big Sur

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

Hi Marc,

The latest versions of PyMOL (e.g. 2.4) work fine on macOS Big Sur.
Old versions of MacPyMOL (until 1.8.6) are not compatible, unfortunately,
and we're not aware of any workarounds to make it work. Upgrading PyMOL is
your only option.

Cheers,
  Thomas


On Mon, Apr 19, 2021 at 8:16 AM Marc Graille <mar...@po...>
wrote:

> Hello,
>
> I have recently updated the iOS of my MacBook Air to Big Sur (version
> 11.2.3) and since then, I cannot use Pymol anymore. This is very annoying
> as it is my favorite program to generate publication grade figures.
>
> Here is the error message I get :
> *This Executable Build integrates and extends Open-Source PyMOL 1.7.2.3.*
> * Detected OpenGL version 2.0 or greater. Shaders available.*
> * Detected GLSL version 1.20.*
> * Detected 8 CPU cores.  Enabled multithreaded rendering.*
> * OpenGL graphics engine:*
> *  GL_VENDOR:   Intel Inc.*
> *  GL_RENDERER: Intel(R) Iris(TM) Plus Graphics OpenGL Engine*
> *  GL_VERSION:  2.1 INTEL-16.1.12*
> *ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns
> err=1281*
>
> My graphics card is : Intel Iris Plus Graphics 1536 Mo.
>
> Any solution to solve this problem?
>
> Thanks a lot for your help,
>
> Yours,
>
> Marc
>
>
> —
> *Marc GRAILLE, PhD*
> DR1-CNRS
> Laboratoire de Biologie Structurale de la Cellule  (BIOC; Ex-Laboratoire
> de Biochimie)
> UMR7654 du CNRS
>
> Head of the team: “Translation and degradation of eukaryotic mRNAs”
>
> *ÉCOLE POLYTECHNIQUE*
> 91128 PALAISEAU CEDEX
> FRANCE
> 📞: +33 (0)1 69 33 48 90
>
>  : mar...@po... / : @GrailleLab
> <https://twitter.com/GrailleLab>
>
> https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes
> —
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] " Global Diffusion Models"

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

(Arun: this is a resent e-mail. My first e-mail was deleted along with spam messages. Thomas Holder asked me to resend it.)

Hi Arun,

I am able to run your script (run ELM_ellipsoid.py) in PyMOL without reported errors or warnings,
and it displays an ellipsoid centered on the hardwired position in the script. It looks like you
need to edit the script to supply the center of mass of your structure, the lengths of the semi-axes
and the orientation of the ellipsoid via three Eulerian angles.

Please be more explicit about what is the "intended" result.
Do you really want the geodesic surfaces in Diffusion_Geometry.png?
The result in ROTDIFF_Ellipsoid looks better.
You can tweak the parameter settings in makeEllipsoid() to make the triangles smaller so that
the surface is smoother.



Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________________
From: Gupta, Arun via PyMOL-users [pym...@li...]
Sent: Wednesday, April 21, 2021 2:51 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] " Global Diffusion Models"

Dear Pymol users

 I am interested in generating the representative figures of Global diffusion geometrical models such as Prolate, Ellipsoid, Oblate or Sphere with overlaid protein PDB of my interest after the Model-free analysis" ( As shown in attached pic). And ROTDIF software provides the desired output pymol script to generate the predicted shape model information.  However, it seems that I am missing some further inputs or Pymol commands  for the correct initialization of the script (attached pic). As, I am not getting the intended results with the script. Can anyone please suggest the correct modifications to the attached script....


Thanks!!!

Arun

Re: [PyMOL] " Global Diffusion Models"

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Arun,

I am able to run your script (run ELM_ellipsoid.py) in PyMOL without reported errors or warnings, 
and it displays an ellipsoid centered on the hardwired position in the script. It looks like you 
need to edit the script to supply the center of mass of your structure, the lengths of the semi-axes
and the orientation of the ellipsoid via three Eulerian angles.

Please be more explicit about what is the "intended" result. 
Do you really want the geodesic surfaces in Diffusion_Geometry.png? 
The result in ROTDIFF_Ellipsoid looks better.
You can tweak the parameter settings in makeEllipsoid() to make the triangles smaller so that
the surface is smoother.


Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________________
From: Gupta, Arun via PyMOL-users [pym...@li...]
Sent: Wednesday, April 21, 2021 2:51 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] " Global Diffusion Models"

Dear Pymol users

 I am interested in generating the representative figures of Global diffusion geometrical models such as Prolate, Ellipsoid, Oblate or Sphere with overlaid protein PDB of my interest after the Model-free analysis" ( As shown in attached pic). And ROTDIF software provides the desired output pymol script to generate the predicted shape model information.  However, it seems that I am missing some further inputs or Pymol commands  for the correct initialization of the script (attached pic). As, I am not getting the intended results with the script. Can anyone please suggest the correct modifications to the attached script....


Thanks!!!

Arun

Re: [PyMOL] Molecular simulation

[Vedat D. <ved...@gm...>]

oh, that's easy, even i can tell you:

on the right panel you have a list of all your loaded molecules. now,
either you click on the "A" (action) field of the molecule you want to
add to another and and select "copy to object" and select the target
structure (which must be visible/activated) from the small popup list,
or, if you want to add a fragment of your source molecule to another,
then you need to select that part and apply the same clicking sequence
to the SELECTION (A>copy...>...).

you can always select fragments of a molecule and apply "copy to
object">"new" in order to have the single objects which you can then
copy into each other using the same mechanism as above.

hope that was clear enough. good luck!

vedat


Am 22.04.21 um 10:39 schrieb Sofiane SAADOUNE:
> Dear users,
>
> I'm user on PyMoL, and i have question.
>
> I have 2 proteins and i would like to merge them on PyMol to create a
> fusion protein . It is possible ? 
> I saw the command " fuse" on https://pymolwiki.org/index.php/Fuse,
> <https://pymolwiki.org/index.php/Fuse,> but i don't know if is only
> for atom or it is also for amino acids ?
>
> Do you have any advice, I take anything that could help me !
>
> Best regards, 
> Saadoune Sofiane
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Molecular simulation

[Sofiane S. <sof...@et...>]

Dear users, 

I'm user on PyMoL, and i have question. 

I have 2 proteins and i would like to merge them on PyMol to create a fusion protein . It is possible ? 
I saw the command " fuse" on [ https://pymolwiki.org/index.php/Fuse, | https://pymolwiki.org/index.php/Fuse, ] but i don't know if is only for atom or it is also for amino acids ? 

Do you have any advice, I take anything that could help me ! 

Best regards, 
Saadoune Sofiane 

[PyMOL] " Global Diffusion Models"

[Gupta, A. <Aru...@wa...>]

Dear Pymol users

 I am interested in generating the representative figures of Global diffusion geometrical models such as Prolate, Ellipsoid, Oblate or Sphere with overlaid protein PDB of my interest after the Model-free analysis" ( As shown in attached pic). And ROTDIF software provides the desired output pymol script to generate the predicted shape model information.  However, it seems that I am missing some further inputs or Pymol commands  for the correct initialization of the script (attached pic). As, I am not getting the intended results with the script. Can anyone please suggest the correct modifications to the attached script....


Thanks!!!

Arun

[PyMOL] Problem with Pymol following update to Mac Big Sur

[Marc G. <mar...@po...>]

Hello,

I have recently updated the iOS of my MacBook Air to Big Sur (version 11.2.3) and since then, I cannot use Pymol anymore. This is very annoying as it is my favorite program to generate publication grade figures.

Here is the error message I get : 
This Executable Build integrates and extends Open-Source PyMOL 1.7.2.3.
 Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 1.20.
 Detected 8 CPU cores.  Enabled multithreaded rendering.
 OpenGL graphics engine:
  GL_VENDOR:   Intel Inc.
  GL_RENDERER: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
  GL_VERSION:  2.1 INTEL-16.1.12
ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1281

My graphics card is : Intel Iris Plus Graphics 1536 Mo.

Any solution to solve this problem?

Thanks a lot for your help,

Yours,

Marc


—
Marc GRAILLE, PhD
DR1-CNRS
Laboratoire de Biologie Structurale de la Cellule  (BIOC; Ex-Laboratoire de Biochimie)
UMR7654 du CNRS

Head of the team: “Translation and degradation of eukaryotic mRNAs”

ÉCOLE POLYTECHNIQUE 
91128 PALAISEAU CEDEX
FRANCE 
📞: +33 (0)1 69 33 48 90

 : mar...@po... <mailto:mar...@po...> / : @GrailleLab <https://twitter.com/GrailleLab>
https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes
—