A year ago, I used Gheorghe Rotaru’s helpful blog post to install PyMOL. Unfortunately, after resetting my computer, I have just discovered that some of the links are broken. Here are the installation steps with new links provided by Christoph Gohlke, who generously offers pre-compiled Windows versions of the latest PyMOL software along with all its requirements.
Install the latest version of Python 3 for Windows:
Download the Windows Installer (x-bit) for Python 3 from their website, with x being your Windows architecture – 32 or 64.
Follow the instructions provided on how to install Python. You can confirm the installation by running ‘py’ in PowerShell.
Download all required wheel files:
You need to download the wheels of Numpy and Pymol.
For numpy, download the latest numpy+mkl files corresponding to the Python version you have installed and the one matching your Windows architecture. For example, for Python 3.12 on a 64-bit Windows, download the
numpy-1.26.3-cp312-cp312-win_amd64.whl file.
Similarly, for Pymol, download the PyMOL launcher and PyMOL itself. Ensure that they match your Python version and Windows architecture.
Install requirements and PyMOL from wheels:
Open a Windows PowerShell instance and change to the directory containing all the .whl files (using the cd command).
Install numpy and PyMOL from the wheels using the following command in PowerShell or follow these instructions:
py -m pip install wheel_file.whlYou should install them in this order:
- Numpy
- PyMOL
- PyMOL launcher
Launch PyMOL:
Now that PyMOL is installed, you can open the PyMOL app by typing the following command in PowerShell:
py.exe -m pymol