Re: [PyMOL] Running PyMOL on a headless machine

[András F. W. <wac...@tt...>]

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
>
>
>
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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