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

[Thomas Holder]

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 
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
>
>  : marc.grai...@polytechnique.edu / : @GrailleLab
> 
>
> https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes
> —
>
>
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Re: [PyMOL] Running PyMOL on a headless machine

[Thomas Holder]

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
 wrote:
>
> Dear fellow PyMOL users,
>
> I have found a solution (at least a workaround):
>
> pymol -cpihq <
> 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 <
> 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
>
>
>
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>
> --
> 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
>
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Re: [PyMOL] Custom selection operators

[Jarrett Johnson]

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  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
>
>
>
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-- 

*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] 
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[PyMOL] Farewell

[Thomas Holder]

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.


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Re: [PyMOL] Farewell

[H. Adam Steinberg]

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  
> 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.
> 
> 
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Re: [PyMOL] Farewell

[David Gae via PyMOL-users]

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  
> 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.
> 
> 
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Re: [PyMOL] Farewell

[Jason Key]

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


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