Install Open Source Pymol in Windows by Conda

Since PyMOL 2.x released, there were no binary installer avaliable for Windows.

PyMOL Wiki provides the way to install open source PyMOL in Windows under Python 2.7.

This post provided the method to install PyMOL 2.x by conda (Anaconda or Minoconda) in Windows.

1. Install Conda

Download Anaconda or Miniconda and install it.

• Note: Although PyMOL Wiki introduced PyMOL for Python 2.7 only, there are also pre-compiled PyMOL distribution for Python 3.x.

2. Create PyMOL envrionment

Click Start menu, and run “Anaconda Prompt”.

conda create -n pymol

Then, activate created environment

conda activate pymol

3. Install supporting packages

# pip
conda install -c anaconda pip

# Numpy
conda install -c anaconda numpy

# PMW
conda install -c conda-forge pmw

All other supporting packages would be installed automatically.

4. Download PyMOL whl files

Download pre-compiled Open-Source PyMOL from Christoph Gohlke of the Laboratory for Fluorescence Dynamics, University of California, Irvine.

Here listed lots of pre-compiled distributions. The filename is:

pymol-2.4.0a0-cp37-cp37m-win_amd64.whl
         \        \          \
          \        \          \__ for 64 bit Windows
           \        \
            \        \___________ for Python 3.7.x 
             \
              \__________________ PyMOL version 2.4.0a0

Download both pymol.whl and pymol_launcher.whl files.

5. Install whl files

• In the conda pymol environment, switch to download directory (e.g., C:\Downloads)

  cd C:\Downloads

• Install pymol_launcher first

  pip install --no-index --find-links="%CD%" pymol_launcher.whl

• It will also install PyMOL automatically.

To updata PyMOL, run

pip install --upgrade --no-deps pymol.whl

• Don’t forget to replace pymol_launcher.whl and pymol.whl by downloaded whl files.
• The pymol_launcher do not need update.

6. Launch pymol

In the activated pymol environment, run

pymol

Then, the PyMOL will be launched.