This page describes how to install PyMOL on Mac OS X.
MacPyMOL is available exclusively to paying sponsors. Schrödinger provides a DMG package which also includes ready-to-use APBS, RigiMOL, an MPEG encoder for movie export, and a small molecule energy minimization engine.
Installation: Drag MacPyMOL.app on the /Applications shortcut. (In principle, you could drag it into any Finder window and run it from there, it doesn’t have to live in /Applications).
Uninstallation: Move /Applications/MacPyMOL.app to Trash
Launching from Command Line
The unix executable resides at /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL
There are two ways to launch the X11 interface:
- rename /Applications/MacPyMOL.app to /Applications/MacPyMOLX11Hybrid.app
- launch the unix executable with the -m flag: /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -m
Stereo on Second Monitor
The trick to getting MacPyMOL to work in stereo on the second monitor is to force it to initially open on that display by providing an appropriate "-X #" (and perhaps -Y #) option on launch. That way the OpenGL context will be created with stereo support.
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 ./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 -Y 100
Source: Warren DeLano; PyMOL Users Archive
# Fink fink install pymol-py27 # MacPorts sudo port install pymol # Homebrew brew install homebrew/science/pymol
Make sure that the dependencies are installed with the required flags:
# MacPorts sudo port install tcl -corefoundation sudo port install tk -quartz # Homebrew brew install Caskroom/cask/xquartz brew install tcl-tk --with-threads --with-x11 brew install python --with-tcl-tk
If PyMOL complains that it wasn't able to find X11, try starting xquartz first, then run pymol from the console.
Problems with precompiled brew installed
This was experienced on date: 2017/06/29, on macOS Sierra 10.12.5.
X11 has been installed with https://www.xquartz.org
There was a problem with tcl-tk from brew, which gave an error Abort trap: 6” error.
This can be confirmed with:
>>> import Tkinter >>> Tkinter.__file__ >>> Tkinter._test()
brew uninstall pymol brew uninstall --ignore-dependencies python brew uninstall tcl-tk
Install from Source
If you want the latest PyMOL code (warning: might include experimental changes), then follow the Linux installation instructions. You will need an environment like Fink, MacPorts or Homebrew to install the dependencies. Make sure you use the appropriate python interpreter (e.g. /sw/bin/python2.7 when using Fink).
Install APBS with Fink
To use the electrostatics plugin, you will need APBS and its dependencies. These are also available as Fink packages, and include APBS, maloc and pdb2pqr. If you have multiple processors available, you might wish to install the MPI version of APBS.
Issuing the command
fink install apbs
will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin.
Some older Macs seem to crash with stereo graphics. If this happens to you, a workaround is to launch PyMOL explicitly in Mono mode with `pymol -M`. You can also set up an alias in your ~/.profile:
alias pymol='pymol -M'