[PyMOL] Error when opening PyMOL installed through Anaconda

[Naveen R. <nav...@gm...>]

Hello all,

I recently brought a new laptop (Windows 11) and had installed Anaconda along with their python interpreter. When it came time to install PyMOL, I saw on the website that it was possible to install PyMOL through Anaconda.

This was very convenient for me, as with my previous laptop (Windows 10), I ran into issues having two python installs on the same device. Installing PyMOL through Anaconda in the base (root) environment would save me from a potential hassle.

I ran the command on the PyMOL website (conda install -c conda-forge -c schrodinger pymol-bundle) in the Anaconda prompt, installing PyMOL in the default environment. When I tried to open PyMOL through the desktop, nothing happens.

However, when I try to open PyMOL through the Anaconda Navigator, I get the following error message:
Traceback (most recent call last):
File "C:\ProgramData\anaconda3\Scripts\pymol-script.py", line 6, in from pymol import launch
File "C:\ProgramData\anaconda3\Lib\site-packages\pymol\__init__.py", line 620, in import pymol._cmd
ImportError: DLL load failed while importing _cmd: The specified module could not be found.

After this error, I installed PyMOL through the installer (to check if it was an issue with the PyMOL version) and it worked. With this in mind I carried out the following troubleshooting steps:

  *   Install PyMOL through Anaconda (with the command from the website) on another PC that has not PyMOL installed before.
  *   Compare the installed packages in the install from Anaconda and from the installer. Resolve the differences in the Anaconda install.
  *   Install PyMOL through Anaconda using other commands I found on the internet, including the one used to install a previous versions of PyMOL.

All of the afformentioned steps were unsucessful in getting the Anaconda install to open.

I have also compared the "__init__.py" from the Anaconda and installer installs and they are the same. I have also attempted to find the "__cmd" file in the installer install but was unsucessful. I am at a loss as to what is causing the installer install to go through but the Anaconda install to fail.

I was hoping if others have a fix for this so that the Anaconda installation opens as I have tried looking for a solution online but failed to find anything useful.

Hope you have a nice day.

Best Wishes,
Naveen Ravichandran