Dear fellow PyMOL users, I have found a solution (at least a workaround):
pymol -cpihq <<EOF import pymol.plugins pymol.plugins.initialize(-1) ... EOFThis 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.pluginspymol.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_innerself.run()File "/opt/miniconda3/envs/gmxbatch/lib/python3.9/threading.py", line 892, in runself._target(*self._args, **self._kwargs)File "/opt/miniconda3/envs/gmxbatch/lib/python3.9/site-packages/pymol/plugins/legacysupport.py", line 134, in starttkapp.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 variableI 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
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