Plugin Manager GUI crash when installing on PyMOL 3.1.0 shipped with PyQt6

[tamir-dingjan]

After attempting to add pymol_plugin/init.py to the Plugin Manager, I get the following traceback:

 PyMOL(TM) Molecular Graphics System, Version 3.1.0.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.

    Created by Warren L. DeLano, Ph.D.

    PyMOL is user-supported open-source software.  Although some versions
    are freely available, PyMOL is not in the public domain.

    If PyMOL is helpful in your work or study, then please volunteer
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.

    More information can be found at "http://www.pymol.org".

    Enter "help" for a list of commands.
    Enter "help <command-name>" for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Detected OpenGL version 2.1. Shaders available.
 Tessellation shaders not available
 Detected GLSL version 1.20.
 OpenGL graphics engine:
  GL_VENDOR:   Apple
  GL_RENDERER: Apple M5
  GL_VERSION:  2.1 Metal - 90.5
 Detected 10 CPU cores.  Enabled multithreaded rendering.

type object 'QFrame' has no attribute 'Sunken'
type object 'QFrame' has no attribute 'Sunken'
Traceback (most recent call last):
  File "/opt/homebrew/lib/python3.14/site-packages/pymol/plugins/managergui_qt.py", line 303, in installplugin
    installPlugin(self)
    ~~~~~~~~~~~~~^^^^^^
  File "/opt/homebrew/lib/python3.14/site-packages/pymol/plugins/legacysupport.py", line 68, in installPlugin
    installPluginFromFile(ofile)
    ~~~~~~~~~~~~~~~~~~~~~^^^^^^^
  File "/opt/homebrew/lib/python3.14/site-packages/pymol/plugins/installation.py", line 199, in installPluginFromFile
    showinfo = tkMessageBox.showinfo
               ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/lib/python3.14/site-packages/pymol/plugins/legacysupport.py", line 140, in __getattr__
    wrapped = getattr(module, name)
  File "/opt/homebrew/lib/python3.14/site-packages/pmg_qt/mimic_tk.py", line 18, in __getattr__
    'askyesno': ('question', QMB.Yes, QMB.No),
                             ^^^^^^^
AttributeError: type object 'QMessageBox' has no attribute 'Yes'

The Plugin Manager window itself does not update or change to reflect the selected file.

[funnirudh]

Getting the same error on M2 Mac with python 3.14.4.

[ekiefl]

Getting the same error on M2 Mac with python 3.14.4.

@funnirudh are you also on PyMOL 3.1?

[funnirudh]

Hi, Apologies for not including this. Yes, I am also on PyMOL 3.1.

[ekiefl]

Can either of you please restart PyMOL and see whether agentic-pymol plugin appears in the Plugin window?

If that's present, I think you successfully installed Agentic PyMOL but encountered a PyMOL bug triggered by the installation.

I'll wait to hear back before drawing any conclusions.

[funnirudh]

Hi, just checked after restarting pymol. No plugin appears. Tried reinstalling and restarting too. Here is the error if that helps:

PyMOL(TM) Molecular Graphics System, Version 3.1.0.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.

Created by Warren L. DeLano, Ph.D. 

PyMOL is user-supported open-source software.  Although some versions
are freely available, PyMOL is not in the public domain.

If PyMOL is helpful in your work or study, then please volunteer 
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.

More information can be found at "http://www.pymol.org".

Enter "help" for a list of commands.
Enter "help <command-name>" for information on a specific command.

Hit ESC anytime to toggle between text and graphics.

Detected OpenGL version 2.1. Shaders available.
Tessellation shaders not available
Detected GLSL version 1.20.
OpenGL graphics engine:
GL_VENDOR: Apple
GL_RENDERER: Apple M2
GL_VERSION: 2.1 Metal - 90.5
Detected 8 CPU cores. Enabled multithreaded rendering.

type object 'QFrame' has no attribute 'Sunken'
type object 'QFrame' has no attribute 'Sunken'
Traceback (most recent call last):
File "/opt/homebrew/lib/python3.14/site-packages/pymol/plugins/managergui_qt.py", line 303, in installplugin
installPlugin(self)
~~~~~~~~~~~~~^^^^^^
File "/opt/homebrew/lib/python3.14/site-packages/pymol/plugins/legacysupport.py", line 68, in installPlugin
installPluginFromFile(ofile)
~~~~~~~~~~~~~~~~~~~~~^^^^^^^
File "/opt/homebrew/lib/python3.14/site-packages/pymol/plugins/installation.py", line 199, in installPluginFromFile
showinfo = tkMessageBox.showinfo
^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/lib/python3.14/site-packages/pymol/plugins/legacysupport.py", line 140, in getattr
wrapped = getattr(module, name)
File "/opt/homebrew/lib/python3.14/site-packages/pmg_qt/mimic_tk.py", line 18, in getattr
'askyesno': ('question', QMB.Yes, QMB.No),
^^^^^^^
AttributeError: type object 'QMessageBox' has no attribute 'Yes'//

[ekiefl]

^^^ Hiding previous conversation to increase visibility on the official diagnosis.

Diagnosis

Ok. First, of all, thanks for the tracebacks.

This is an upstream PyMOL bug, not an agentic-pymol problem, and it affects every Homebrew PyMOL 3.1.0 install

Homebrew's pymol 3.1.0 formula depends on pyqt (PyQt6, currently 6.11.0) on python@3.14, but that PyMOL build's bundled plugin-installer code was still written for PyQt5's enums. PyQt6 moved those enums into nested classes (e.g. from QMessageBox.Yes to QMessageBox.StandardButton.Yes), so PyMOL's own installer GUI crashes before it can copy plugin files. Any plugin fails to install this way on this build.

(Note: this is about the Qt binding, not the version number. The same PyMOL 3.1.0 packaged against PyQt5 — e.g. the Flatpak — doesn't hit this. It's Homebrew's PyQt6 dependency that triggers it.)

The exact failure is tracked upstream and already fixed:

• Bug report: Edits missing for PyQT6 support schrodinger/pymol-open-source#498 - Originally reported on Fedora
• Fix: commit schrodinger/pymol-open-source@87d27da - Fix in PyMOL master but not in release

Workaround: install the plugin without the broken GUI

PyMOL auto-loads any plugin in its startup directory, so you can install by copying the package there directly. Paste this into the PyMOL command line (replace the path with your local clone):

import shutil
from pathlib import Path
import pymol.plugins

src = Path("your/absolute/path/to/agentic-pymol/pymol_plugin") # <<<< Edit this line
dst = Path(pymol.plugins.get_startup_path()[0]) / "pymol_plugin"
dst.parent.mkdir(parents=True, exist_ok=True)
shutil.copytree(src, dst, dirs_exist_ok=True)
print("Installed to", dst)

Then restart PyMOL. "agentic-pymol plugin" should appear under the Plugin menu, and Plugin → agentic-pymol plugin → Start Listening will work as documented.

Alternatively, don't use a 3.1.0 install that ships with PyQt6.

The real solution: wait

Once Homebrew ships a PyMOL build that includes the upstream Qt6 fix, the normal Install New Plugin flow will work again. We'll also add this manual-install path to the README so others on PyQt6 builds aren't blocked.

[ekiefl]

Can I bother either of you to test out the workaround? Thanks!

[funnirudh]

Yep. Can confirm this workaround works! Thank you.

[tamir-dingjan]

Thanks for the quick turnaround, can confirm this works for me too 👍