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[[Category:Installation|Mac]]
This page describes how to install PyMOL on Mac OS X.
http://images.apple.com/powermac/images/solutionsscience20050427.jpg
 
== Incentive PyMOL ==
 
[http://www.schrodinger.com Schrödinger] provides pre-compiled PyMOL to paying sponsors. The bundle also includes ready-to-use [[APBS]], [[morph|RigiMOL]], an MPEG encoder for movie export, and a small molecule energy minimization engine.
 
Download: https://pymol.org/
 
Installation: Drag '''PyMOL.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/PyMOL.app''' to Trash
 
=== Launching from Command Line ===
 
The unix executable resides at '''/Applications/PyMOL.app/Contents/MacOS/PyMOL'''
 
=== X11 Hybrid ===
 
''Applies to PyMOL 1.x, not to PyMOL 2.x''
 
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 [[Plugins|Plugin]] menu and the [[Builder]].
 
Requires [http://xquartz.macosforge.org/ XQuartz].
 
There are two ways to launch the X11 interface:
# Rename or copy/duplicate '''/Applications/MacPyMOL.app''' to '''/Applications/MacPyMOLX11Hybrid.app''' or to '''/Applications/PyMOLX11Hybrid.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.
<source lang="python">
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000
./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 -Y 100
</source>
 
'''Source:''' [https://sourceforge.net/p/pymol/mailman/message/11671952/ Warren DeLano; PyMOL Users Archive]
 
== Open-Source PyMOL ==
 
=== Package managers ===


__TOC__
Open-Source PyMOL is available [https://github.com/schrodinger/pymol-open-source/blob/master/LICENSE free of charge] and may be readily installed via the [http://brew.sh/ Homebrew] (recommended), [https://www.macports.org/ MacPorts], or [http://www.finkproject.org/ Fink] package managers.


=Installing MacPyMOL=
<source lang="bash">
http://delsci.com/macpymol/macpymol350.jpg
# Homebrew (recommended)
brew install brewsci/bio/pymol


===Essentials===
# Fink
fink install pymol-py27


The [http://delsci.com/macpymol/ download] is about as straightforward as it gets, and you can install it wherever that makes you happy.
# MacPorts
sudo port install pymol
</source>


I wrote a [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable that lives in MacPyMOL.app/Contents/MacOS/PyMOL and pass arguments to it.
You may need to make sure that the dependencies are installed with the required flags, e.g. for MacPorts:


===Extras===
<source lang="bash">
# MacPorts
sudo port install tcl -corefoundation
sudo port install tk -quartz
</source>


====PowerMate Dial====
If PyMOL complains that it wasn't able to find X11, try starting xquartz first, then run pymol from the console.


The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].
=== Install from Source ===


http://www.griffintechnology.com/images/products/prod_powermate_a.jpg
If you want the latest PyMOL code (warning: might include experimental changes), then follow the [[Linux_Install#Install_from_source|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).


====Stereo====
To run PyMOL with a native PyQt library (linked against macOS OpenGL framework, not against XQuartz), it needs to be built with the <code>--osx-frameworks</code> option:


The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support stereo in a window.
<source lang="bash">
python setup.py --osx-frameworks install
</source>


=Installing X-windows based pymol on Mac OS X=
=== Install APBS with Fink ===


===Why would you want to do this?===
To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies.  These are also available as Fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs APBS], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi-openmpi MPI version of APBS].


#You want to run a free, guilt-free, open-source version of pymol
Issuing the command
#You just happen to prefer the tkinter menu
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/  apbs plugin] for free grasp-like electrostatic calculations.


===Simplest Installation===
fink install apbs


By far the simplest way to install the X-windows based version of pymol on OS X is by using the fink package management system.  To compile it, all you need to do is issue the command
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.


fink install pymol-py24
=== 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:
(This will install python2.4 in fink, along with an X-windows based tkinter. There are also versions that permit you to install pymol to interact with python2.3 and even python2.2.  Fink uses its own unix-type python installation, but you can trick pymol into using the aqua framework to get a prettier GUI after the fact.)


The [http://pdb.finkproject.org/pdb/package.php/pymol-py24 fink pymol package] currently exists in the unstable branch of fink, so you will either have to activate the unstable branch or make the following symbolic links:
alias pymol='pymol -M'


sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.
== See Also ==
You might need to create the latter directory if it doesn't already exist, i.e., issue the command


sudo mkdir -p /sw/fink/dists/local/main/finkinfo
* [[pymolrc]]
* [[Linux Install]]
* [[Windows Install]]
* [[MovieSchool_6#Exporting_your_Movie|FreeMOL installation for MPEG movie export]]
* [[User:Wgscott|Bill Scott’s]] [[MacOSX-specific .pymolrc file]] and his crystallographic software [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].
* [[Launching_PyMOL#MacOS_X]]


===Eye-Candy Tweaks===
[[Category:Installation|Mac]]
[[Category:Nucleic_Acids|MAC Install]]
[[Category:Technical Issues|MAC Install]]
[[Category:Mac|MAC Install]]

Latest revision as of 12:05, 8 October 2018

This page describes how to install PyMOL on Mac OS X.

Incentive PyMOL

Schrödinger provides pre-compiled PyMOL to paying sponsors. The bundle also includes ready-to-use APBS, RigiMOL, an MPEG encoder for movie export, and a small molecule energy minimization engine.

Download: https://pymol.org/

Installation: Drag PyMOL.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/PyMOL.app to Trash

Launching from Command Line

The unix executable resides at /Applications/PyMOL.app/Contents/MacOS/PyMOL

X11 Hybrid

Applies to PyMOL 1.x, not to PyMOL 2.x

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:

  1. Rename or copy/duplicate /Applications/MacPyMOL.app to /Applications/MacPyMOLX11Hybrid.app or to /Applications/PyMOLX11Hybrid.app
  2. 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

Package managers

Open-Source PyMOL is available free of charge and may be readily installed via the Homebrew (recommended), MacPorts, or Fink package managers. 

# Homebrew (recommended)
brew install brewsci/bio/pymol

# Fink
fink install pymol-py27

# MacPorts
sudo port install pymol

You may need to make sure that the dependencies are installed with the required flags, e.g. for MacPorts: 

# MacPorts
sudo port install tcl -corefoundation
sudo port install tk -quartz

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).

To run PyMOL with a native PyQt library (linked against macOS OpenGL framework, not against XQuartz), it needs to be built with the --osx-frameworks option: 

python setup.py --osx-frameworks install

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

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