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
<wacha.and...@ttk.hu> 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/pymol-users@lists.sourceforge.net
> 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/pymol-users@lists.sourceforge.net
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe:
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
