Open Source PyMOL for Windows

Open source PyMOL is available free of charge. A pre-compiled open source PyMOL is available free from Christoph Gohlke of the Department of Biomedical Engineering, University of California, Irvine.

This repository provides a method to install PyMOL v2.6 on Windows. If necessary, a portuguese version of this guide is available here.

Download & Installation

Follow these steps to install PyMOL v2.6:

1. Install the latest version of Python (v3.12.x) for Windows from here.

Note: Make sure the option to add environment variables is selected or add the folder of python.exe to system PATH.

2. Install required Python packages

python -m pip install numpy
python -m pip install pmw
python -m pip install pyqt5

3. Download pre-compiled Open-Source PyMOL wheel files, compatible with Python 3.12 and Windows 64-bit, from the links below:

• pymol-launcher
• pymol

Note: You can check Python version on anaconda by typing python --version.

If you are using a different Python version or Windows 32-bits, please there are other pre-compiled versions here.

The filename structure is the following:

pymol‑2.6.0a0‑cp312‑cp312‑win_amd64.whl
         \         \          \
          \         \          \___ for 64 bit Windows
           \         \
            \         \____________ for Python 3.12.x
             \
              \____________________ PyMOL version 2.6.0a0

4. Install wheel files

In the CMD window (not PowerShell!), switch to download directory (C:\Users\<Your Username>\Downloads):

cd Downloads

Then, install pymol_launcher-2.6-cp312-cp312-win_amd64.whl by typing:

python -m pip install --no-index --find-links="%CD%" pymol_launcher-2.6-cp312-cp312-win_amd64.whl

Finally, to install pymol-2.6.0a0-cp312-cp312-win_amd64.whl, run:

python -m pip install --upgrade --no-deps pymol-2.6.0a0-cp312-cp312-win_amd64.whl

Note: If you downloaded different files in Step 4, replace pymol_launcher-2.6-cp312-cp312-win_amd64.whl and pymol-2.6.0a0-cp312-cp312-win_amd64.whl by the downloaded wheel files.

5. Launch PyMOL v2.6

In the CMD window (not PowerShell!), run:

where.exe pymol
pymol

Then, PyMOL v2.6 will be launched and ready to go.

6. (Optional) Create a shortcut to PyMOL

where.exe pymol

The location of pymol.exe will be displayed. Navigate to the file location, right-click on PyMOL.exe, and copy it to your Desktop.