Thursday, September 15, 2016

Installing Latest PyMOL Software for FREE


Introduction to PyMOL

PyMOL is a Python-enhanced OpenGL based molecular visualization tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is available at ( for free to everyone. The commercial graphical end PyMOL is developed, maintained and distributed by Schrödinger, Inc ( PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. According to the original author, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL.

Requirements for PyMOL Installation

In this tutorial, I have explained how to install the latest PyMOL software (the latest version of PyMOL software as on September 15, 2016 is for free. I have chosed Windows 10 Enterprise OEM 64-bit operating system to install the PyMOL software. So, I have downloaded all stable version executables in 64-bit. Before begining to install the PyMOL, we have to download the Python software and needed Python packages with same version. For example, I have chosen Python version 3.x, So I have downloaded the Python packages supporting 3.x version and x64(64-bit).

1. Python v3.5.2 - (File Size: 28.7 MB)

Download PyMOL and neccessary packages from the unofficial windows binaries portal (

2. PIP v8.1.2 - (File Size: 1.14 MB)

3. Numpy+MKL v1.11.1 - (File Size: 111 MB)

4. PMW v2.0.1 - (File Size: 533 KB)

5. PyMOL v1.8.3.2 - (File Size: 7.03 MB)

6. PyMOL Launcher v1.0 - (File Size: 207 KB)

Total download size of the complete softwares will be around 148.61 MB.

Installation Procedure

1. Install the downloaded Python v3.5.2 sofware with administrator priviliges. Follow the Customize installation procedure as shown in the images below to change the installation directory.

2. Copy the downloaded Python packages PIP v8.1.2, PMW v2.0.1, PyMOL v1.8.3.2, PyMOL v1.0, PyMOL Launcher v1.0, and Numpy+MKL v1.11.1 to the directory (C:\Python35\Scripts).

3. Run Command Prompt with administrator priviliges. Enter the command line (cd "C:\Python35\Scripts") to enter into Scripts directory.

4. Enter the following commands in the Commmand Prompt in the order given below to install PyMOL. Refer the snapshot given below for clarification.
  • pip install pip-8.1.2-py2.py3-none-any.whl
  • pip install numpy-1.11.1+mkl-cp35-cp35m-win_amd64.whl
  • pip install Pmw-2.0.1-py3-none-any.whl
  • pip install pymol-
  • pip install pymol_launcher-1.0-cp35-cp35m-win_amd64.whl
5. Open the directory (C:\Python35) and double-click the binary file PyMOL.exe to launch PyMOL v1.8.3.2 software.


  1. Dear Ashok Kumar T.,

    Thank you for this tutorial. I followed your instructions with my own configurations, I used Python 3.6 and cp36 x32 files. I managed to install everything and I can run PyMOL 1.8.6 but I have an issue with the external GUI who doesn't show. I tried to search for an answer to my problem and I think it has something to do with pmg_tk but I don't know anything about Python and I didn't manage to fix my problem.

    Do you have any clue on the way to fix it ?

    Thank you very much for your tutorial,
    Alexis M.

    1. Uninstall Python software, clean installed directory, clean registry, etc. Download latest Python software and packages compatible to OS (OS bit, Python version supported packages, etc.). Install software/packages in order as mentioned in the article. Carefully select the check boxes as shown in the figure 1, 2, and 3. before installation.