Installing open source PyMol on a Mac

This is a quick “how to” post. There is a licensed version of PyMol (MacPyMol) available, but the open source version can be installed on a Mac free of charge. The official page has a guide, which is not terribly detailed, and I found this excellent guide which is unfortunately out-of-date.

Here is an updated guide to installing PyMol using Homebrew on macOS Mojave 10.14.3

Step 1 is to install Homebrew

/usr/bin/ruby -e "$(curl -fsSL"

Next step is to install the PyMol dependencies using Homebrew

brew install Caskroom/cask/xquartz
brew install tcl-tk
brew install python

Now install PyMol.

brew install brewsci/bio/pymol

You can now run PyMol by typing


The MPIBR-Bioinformatics page has the following guide to make a little executable app to launch PyMol straight from the Desktop.

  • Open Automator, which is in Applications in macOS.
  • Create new document, select “Application”.
  • Select “Actions” and “Library” in the left pane. Select “Utilities” and “Run Shell Script”. Drag this into the main pane.
  • Choose “/bin/bash” as a shell.
  • Paste the following: /usr/local/bin/pymol -M. If this doesn’t work, check the path to pymol using which pymol in the terminal, and use this instead.
  • Save the application (“File > Save”) to the Desktop and name it “PyMol”.

Now you can double-click this app to run PyMol.

18 thoughts on “Installing open source PyMol on a Mac

  1. Hi,

    Just installed PyMOL the way you specified, however because tcl-tk is built without x11 support, all legacy plugins running on PyMOL won’t work. Do you have any workaround?

  2. Thank you so much for this, I tried to install pymol directly from SourceForge and had many conflicts with X11 versions, this solved all my problems.

  3. HI, I’m following the steps and when try brew pymol it’s failed, show this notif

    A full installation of is required to compile
    this software. Installing just the Command Line Tools is not sufficient.

    any suggestion?
    thanks alot
    I’m using 10.11 el capitan mac.

  4. Hi everyone. I am on High Sierra and trying to install Pymol.
    HAs anyone out there has done this or has suggestions for installation?
    Thanks a lot!

  5. I follow the guide provided above but my installation of ‘brew install brewsci/bio/pymol’ keeps stopping at the following line

    ==> python3 install –install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin –install-lib=/usr/local/Cell

    and then nothing happens for hours. Is something wrong? And how do i fix it!?

  6. Thanks so much, you are a lifesaver! I managed to instal it on my Mac running Catalina without much difficulty.

    The only small issue is that after the first command I got this message from terminal:

    Warning: The Ruby Homebrew installer is now deprecated and has been rewritten in Bash. Please migrate to the following command:
    /bin/bash -c “$(curl -fsSL”

    So I used the recommended command and completed the installation with the other commands in your guide.

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