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Difference between revisions of "MAC Install"
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=== Install from Source === | === Install from Source === | ||
Revision as of 12:59, 29 June 2017
This page describes how to install PyMOL on Mac OS X.
Incentive PyMOL
MacPyMOL
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.
Download: http://pymol.org/download
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
X11 Hybrid
MacPyMOL can optionally run with the same two-window GUI which PyMOL uses on Windows and Linux. This GUI has some additional features, like the Plugin menu and the Builder.
Requires XQuartz.
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
Open-Source PyMOL
Pre-compiled
Pre-compiled Open-Source PyMOL is available free of charge with the MacPorts, Fink and Homebrew environments.
# 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.
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.
Stereo issues
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'
See Also
- pymolrc
- Linux Install
- Windows Install
- FreeMOL installation for MPEG movie export
- Bill Scott’s MacOSX-specific .pymolrc file and his crystallographic software wiki and website, including instructions on how to install precompiled binary packages using fink.
- Launching_PyMOL#MacOS_X