Public bug reported:
The pymol-3.1.0+dfsg package under the default Wayland server has
regressions in the use of the APBS Electrostatics plugin in both plucky
and if the same packaging is built under oracular. The issue can be
reproduced as follows...
1) After installing the pymol-3.1.0+dfsg package also install the apbs and
pdb2pqr packages
2) execute 'pymol' from the terminal window
3) Select the File->Get PDB... menu item
4) Enter '1AJ4' in the PDB ID field and click the Download button in the dialog
box
5) Select the Plugin->APBS Electrostatics menu item
6) Click on the Run button in the APBS Electrostatics dialog that appears..
7) this will cause pymol to crash under Wayland with the following messages in
the terminal window...
WARNING:Ignoring 392 header lines in output.
Tempdir: /tmp/tmpn0xnoyyn
Save: wrote "/tmp/tmpn0xnoyyn/mol.pqr".
GL_ERROR : 0x0502 GenericBuffer::genBuffer failed
terminate called without an active exception
Aborted (core dumped)
This issue doesn't exist under the X11 server on either plucky or
oracular
ps One other issue under Wayland with pymol-3.1.0+dfsg is that the pymol
console window doesn't show the expected...
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 4.6. Shaders available.
Detected GLSL version 4.60.
OpenGL graphics engine:
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: NVIDIA GeForce GTX 1050/PCIe/SSE2
GL_VERSION: 4.6.0 NVIDIA 560.35.03
Detected 12 CPU cores. Enabled multithreaded rendering.
when pymol is started from the terminal. You can force this to be shown
by clicking back in the terminal window where pymol was launched and
then clicking back on the pymol window.
Given the regressions, you might consider reverting plucky back to the
pymol 3.0.0 which has neither issue with Wayland.
** Affects: pymol (Ubuntu)
Importance: Undecided
Status: New
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https://bugs.launchpad.net/bugs/2106189
Title:
pymol-3.1.0+dfsg wayland regressions
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