[PyMOL] Displaying internal cavities as a surface or a mesh

Hi, Apologies if this is a rudimentary question. I'd like to display an internal binding pocket around a compound as a surface (or mesh). I don't need to detect the presence of a cavity but simply show its approximate boundaries. 1. Is there a way to display the cavity as a surface about spe

[PyMOL] Align in PyMOL via Python script

Hi, I would like to run the Align Python script found on the Align page of the PyMOLwiki (https://pymolwiki.org/index.php/Align). I've tweaked it slightly for my uses and it seems to run fine on PyMOL 2.5.0 but according to the wiki it should output a list of results (RMSD etc) in the internal

Re: [PyMOL] Align in PyMOL via Python script

cmd: align x, y output: ... Executive: RMSD =4.030 (10847 to 10847 atoms) cmd: print(cmd.align("x", "y")) output: (4.0296430587768555, 10847, 5, 24.87837028503418, 13476, 1234.0, 1192) Bests, Tamas On 2023. 03. 02. 8:54, Irwin Selvam wrote: Hi, I would like to run the Align

[PyMOL] Caver3 plugin failure to initialise

Hi all, I'm trying to run the Caver3 plugin on PyMOL 2.5.7 on an M2 mac (Sequoia 15.3) but it's failing to initialise due to the "tkinter" module being missing. I've updated python to 3.13.2, which should come with tkinter 8.6. Does anyone have a solution? Cheers, Irwin ___

Re: [PyMOL] Caver3 plugin failure to initialise

Hi, Unfortunately, I'm still getting the same error ("no module named tkinter") and a failure to initialise. Any ideas? Cheers, Irwin From: Jarrett Johnson Sent: 17 February 2025 00:33:26 To: Irwin Selvam Cc: pymol-users@lists.sourceforge.

Re: [PyMOL] Caver3 plugin failure to initialise

Hi Jarrett, The issue was I downloaded the "master" zip linked in the instructions subsection of the github page. Using the "pyqt" zip linked from the code button worked. Cheers, Irwin From: Jarrett Johnson Sent: 27 February 2025 11:20