PyMOL Installation

For this course we will use the open-source version of PyMOL. Please follow the instructions for your operating system below.

Note: I will be using PyMOL 2.x on my own machine, but everything we do in class will work the same in PyMOL 3.1.

1. Windows: Install PyMOL (Open-Source 3.1)

  1. Download the Windows installer (64-bit) from this link:
    Download PyMOL Open Source v3.1.0.4+1 for Windows (64-bit)
  2. Once the download is finished, double-click the file PyMOL_Open_source_v3.1.0.4+1_WINx64_setup.exe.
  3. Follow the installer prompts (you can accept the default options).
  4. After installation completes, you should find PyMOL in the Start menu. Start it and make sure it opens without errors.

2. macOS: Install PyMOL 3.1 Using Homebrew

On macOS we will install PyMOL using Homebrew, a package manager for Mac. If you already have Homebrew installed, you can skip step 1.

Step 1: Install Homebrew (if needed: type "which brew" in a terminal window. If it says, "/usr/local/bin/brew", you don't need to install brew. Skip this step.)

  1. Open the Terminal application (Applications → Utilities → Terminal).
  2. Paste this command into Terminal and press Enter: 
    /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
  3. Follow the on-screen instructions. You may need to enter your macOS password.

Step 2: Install PyMOL with Homebrew

  1. In the same Terminal window (or a new one), run: 
    brew install pymol
  2. Wait for the installation to finish. This will install the open-source PyMOL 3.1 package.
  3. After installation, you can start PyMOL in two ways:
    • From Terminal:
      Type pymol and press Enter.
    • From Finder/Launchpad (if linked):
      On some setups you may also find a PyMOL app icon. If not, using Terminal with pymol is fine.
If the command pymol is “not found”:
Close Terminal, open a new Terminal window, and try again. If it still doesn’t work, please send me the exact error message.

3. (Optional) Advanced: PyMOL via pip

This option is mainly for people who are already comfortable with Python and pip. For most people, the Windows installer or Homebrew is easier and recommended.

  1. Make sure you have a recent Python 3 installed on your system.
  2. Open a terminal (Command Prompt on Windows, Terminal on macOS).
  3. Install the open-source PyMOL package: 
    pip install pymol-open-source
  4. After installation, try running: 
    pymol

    If that does not work, you may need to adjust your PATH or use: 

    python -m pymol