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The official page has a guide, which is not terribly detailed, and I found this excellent guide which is unfortunately out-of-date.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 https://raw.githubusercontent.com/Homebrew/install/master/install)"

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

pymol

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.

26 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 Xcode.app 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 setup.py 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!?

      1. I have just checked. I get the following output:

        /Library/Frameworks/Python.framework/Versions/3.8/bin/python3

  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 https://raw.githubusercontent.com/Homebrew/install/master/install.sh)”

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

  7. Great post, Thanks!. I just set this up. I wanted to be able to select this “pseudo-application” as the default option for PDBs (i.e. the “Open with” default) so that I could click on a PDB file and it would open the OpenSOurce PyMOL and load the PDB.

    I achieved this by modifying your script a bit. Change the “pass input” option to arguments, then change the script to include the additional option: /usr/local/bin/pymol -M “$@”

    Now, when I click on a pdb file, it opens it in OpenSource Pymol

  8. I am having problems installing PyMOL on my mac with the commands in Homebrew provided above. I am running MacOS Catalina. Anybody experiencing similar problems?

  9. I just wanted to comment on a few things to check if the above guide does not work for you. Firstly, the latest PyMOL (2.5.0 at the time of writing) runs on macOS Big Sur 11.6.1. However, I have run into some problems after doing some brew updates. In one case this lead to PyMOL launching but then crashing and in the other, PyMOL launched but was missing the menu bar.

    So two things to check: is XCode installed on your system? I haven’t been able to confirm but I suspect it is needed. Second, if you get errors when PyMOL launches and/or it prints that “Qt not available, using … interface”. Then a fix I found works was to `pip3 install PySide2`. This installed PySide2-5.15.2 shiboken2-5.15.2 on my system and allowed successful launch of PyMOL.

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