Now you can double-click this app to run PyMol. I installed XQuartz in OS X El Captain using the following command: brew install Caskroom/cask/xquartz After completion, brew list does not show XQuartz. Save the application (“File > Save”) to the Desktop and name it “PyMol”.If this doesn’t work, check the path to pymol using which pymol in the terminal, and use this instead. Paste the following: /usr/local/bin/pymol -M.Select “Utilities” and “Run Shell Script”. Select “Actions” and “Library” in the left pane.Create new document, select “Application”.Open Automator, which is in Applications in macOS.The MPIBR-Bioinformatics page has the following guide to make a little executable app to launch PyMol straight from the Desktop. Next step is to install the PyMol dependencies using Homebrew brew install Caskroom/cask/xquartz Step 1 is to install Homebrew /usr/bin/ruby -e '$(curl -fsSL )' Here is an updated guide to installing PyMol using Homebrew on macOS Mojave 10.14.3 The official page has a guide, which is not terribly detailed, and I found this excellent guide which is unfortunately out-of-date. There is a licensed version of PyMol (MacPyMol) available, but the open source version can be installed on a Mac free of charge. Alternatively, you can make symbolic links to matlab and mex executable in /usr/local/bin thanks to the command sudo ln -s Applications/MATLAB_RXXXX.app/bin/matlab matlab and sudo ln -s Applications/MATLAB_RXXXX.app/bin/mex mex.This is a quick “how to” post. If not, add Applications/MATLAB_RXXXX.app/bin on your path (for instance with export PATH=$PATH:Applications/MATLAB_RXXXX.app/bin if your shell is bash and for XXXX your Matlab installed version. The compilation of the Matlab interface (with the -enable-matlab option of the configure script) may fail due to a bad configuration of the Matlab compiler mex.įirst, you need matlab and mex commands accessible from your shell prompt. You can simply use the addpath command in the octave command line. You can put addpath('toolbox_dir', '-begin') to your $HOME/.octaverc file The last step is to add the path to the toolbox in the octave path: The compilation of the Octave interface is performed with the -enable-octave option of the configure script.įirst, you need octave and mkoctfile commands accessible from your shell prompt (for instance invoking brew install octave). Note that there are other options to the configure script.

Install xquartz homebrew