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Open Source PyMOL for macOS

Open source PyMOL is available free of charge and may be installed via the Homebrew package manager.

This repository provides a method to install PyMOL v2.6 on macOS. If necessary, a portuguese version of this guide is available here.

Download & Installation

Follow these steps to install PyMOL v2.6:

  1. Install Homebrew:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
  1. Install PyMOL dependencies (python, xquartz, tcl-tk, Qt5) using Homebrew:
brew install Caskroom/cask/xquartz
brew install tcl-tk
brew install python
pip install pyqt5
  1. Install PyMOL
brew install brewsci/bio/pymol
  1. Create an application executable for PyMOL:
  • 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”.
  1. Launch PyMOL v2.6

In the terminal, run:

pymol

or, you can start PyMOL by double clicking the created application in the desktop.