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B7H7D7

Member

Registered: 2018-01-19

Posts: 34

pymol not working correctly

I installed pymol on a new machine (Linux kawa 6.9.3-arch1-1 #1 SMP PREEMPT_DYNAMIC Fri, 31 May 2024 15:14:45 +0000 x86_64 GNU/Linux). It accepts commands such that pymol --help but for pymol launched alone or pymol somefile.pdb I get the following :

PySide2/__init__.py: Unable to import shiboken2 from ,  /usr/lib/python3.11/site-packages, /usr/lib/python312.zip, /usr/lib/python3.12, /usr/lib/python3.12/lib-dynload, /usr/lib/python3.12/site-packages
Qt not available (pymol.Qt), using GLUT/Tk interface
Traceback (most recent call last):
  File "/usr/lib/python3.12/site-packages/pymol/__init__.py", line 73, in <module>
    sys.exit(pymol.launch(args))
             ^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/site-packages/pymol/__init__.py", line 429, in launch
    _cmd.runpymol(None, block_input_hook)
NotImplementedError: compile with --glut

although shiboken2 seems installed in /usr/lib/python3.11/site-packages/ :

: ll /usr/lib/python3.11/site-packages/shiboken2/
-rw-r--r-- 1 root root   146 Mar 15 12:01 _config.py
drwxr-xr-x 3 root root  4096 Nov  3  2023 files.dir
-rw-r--r-- 1 root root  2461 Mar 15 12:01 _git_shiboken_module_version.py
-rw-r--r-- 1 root root   745 Mar 15 12:01 __init__.py
-rw-r--r-- 1 root root    33 Mar 15 12:01 py.typed
-rwxr-xr-x 1 root root 18984 Mar 15 12:01 shiboken2.cpython-311-x86_64-linux-gnu.so
-rw-r--r-- 1 root root  1669 Mar 15 12:01 Shiboken.pyi

Please, what do do ?
P.

whitie

Member

Registered: 2011-03-13

Posts: 23

Re: pymol not working correctly

The current Python version is 3.12. You must rebuild your AUR packages for the new Python version.

Greets
Whitie

B7H7D7

Member

Registered: 2018-01-19

Posts: 34

Re: pymol not working correctly

Hi Whitie.
pymol is not an AUR package but a standard one installed using pacman -S pymol.

I have no possibility do do that. Only the maintainers can do what you suggest.
P.

Last edited by B7H7D7 (2024-07-09 12:22:54)

whitie

Member

Registered: 2011-03-13

Posts: 23

Re: pymol not working correctly

Ah yes, I have found it. PyMOL requires python-pyqt5, maybe the wrapper for PySide is outdated. Try to remove PySide2 and shiboken2 and install python-pyqt5 instead.

B7H7D7

Member

Registered: 2018-01-19

Posts: 34

Re: pymol not working correctly

Right. python-pyqt5 is required.

The main window is now displayed but the molecules are not fully represented and mouse actions are not understood.
I will try to remove PySide2 and shiboken2 as you suggested.

But thanks,
P.

B7H7D7

Member

Registered: 2018-01-19

Posts: 34

Re: pymol not working correctly

PySide2 and shiboken2 removed.
Mouse actions seen but not executed correctly.

Note that jmol works perfectly.

Where is the problem ?
P.

Last edited by B7H7D7 (2024-07-10 06:42:32)