If you are on Ubuntu, installing PyMOL is as easy as sudo apt-get install pymol. Unfortunately, almost all students in my medicinal biochemistry course use Windows as their OS (why?!). This page contains a “followable” set of instructions to install PyMOL on Windows. Note that you could use the PyMOL installation from Schrodinger, but you need a paid licence for that (yuck!).

So, first we a Python interpreter. PyMOL is written in the Python programming language, hence you need this to run PyMOL.

1. Download Python 3.7.2 from the Python website (the file you want is called Windows x86-64 executable installer).
2. Run the downloaded file and select the customized installation. Leave everything as is, with the exception of the install location. Set this to C:\Python37

PyMOL is a complex bit of software and requires some other libraries which we need to install.

1. From the PyMOL section on the Gohlke page, download the file pymol‑2.3.0‑cp37‑cp37m‑win_amd64.whl in directory C:\pymol_installation. You need to create this directory first from Windows Explorer.
2. Under the PyMOL section on the Gohlke page, also download the file pymol_launcher‑2.1‑cp37‑cp37m‑win_amd64.whl in directory C:\pymol_installation.

You should now have two files in your C:\pymol_installation directory.

1. Open a Command Prompt. Search for the Command Prompt, right-click and click on Run as administrator option.
2. In the command prompt execute pip install wheel.
3. In the command prompt execute pip install –upgrade pip
4. Go to the PyMOL installation directory cd \pymol_installation
5. Run the command pip install pymol-2.3.0-cp37-cp37m-win_amd64.whl
6. Run the command pip install pymol_launcher-2.1-cp37-cp37m-win_amd64.whl

To run PyMOL you just need to type pymol in the Command Prompt. Alternatively, browse your C:\Python37 directory, right-click on the file pymol.exe and select the option Send to followed by Desktop (create shortcut. You can now access PyMOL by clicking on the PyMOL icon on your desktop.