Install Open Source PyMOL 3.0.x in Windows 11

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Open-source wheels for PyMOL 3.0.x have been released in April 9, 2024, and the software distribution method has been changed. Former installation methods 1 2 could not work at all. Here provides a new walk through to install open-source PyMOL 3.0.x in Windows 11.

1. Install Miniconda for Windows

First install Miniconda for Windows as described in a previous post.

2. Create an environment for PyMOL

Create a conda environment for PyMOL 3.0.x:

(base) C:\Users\username>conda create -n pymol-3.0 python=3.12 pip

Then activate this environment and install necessary packages:

(base) C:\Users\username>conda activate pymol-3.0

# Install necessary packages
(pymol-3.0) C:\Users\username>python -m pip install numpy pmw pyqt5

3. Download wheel file and install PyMOL

Pymol-open-source wheels for Python on Windows have been released in a GitHub repository cgohlke/pymol-open-source-wheels, which can be downloaded from the release page.

For Windows 11 x64, download pymol-3.0.0-cp312-cp312-win_amd64.whl.

Now install as:

(pymol-3.0) C:\Users\username>python -m pip install pymol-3.0.0-cp312-cp312-win_amd64.whl

Please note the path of this wheel file.

If there were no error message, launch PyMOL via:

(pymol-3.0) C:\Users\username>pymol

Have fun!


  • It looks the pymol_launcher is no longer needed. This is different from previous installation methods.