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| − | [[ | + | This page describes how to install PyMOL on Mac OS X. |
| − | http:// | + | |
| + | == 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 === | |
| − | + | 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. | |
| − | http:// | ||
| − | = | + | <source lang="bash"> |
| + | # Homebrew (recommended) | ||
| + | brew install brewsci/bio/pymol | ||
| − | + | # Fink | |
| + | fink install pymol-py27 | ||
| − | + | # MacPorts | |
| + | sudo port install pymol | ||
| + | </source> | ||
| − | + | You may need to make sure that the dependencies are installed with the required flags, e.g. for MacPorts: | |
| − | = | + | <source lang="bash"> |
| + | # MacPorts | ||
| + | sudo port install tcl -corefoundation | ||
| + | sudo port install tk -quartz | ||
| + | </source> | ||
| − | + | 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_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). | |
| − | + | 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: | |
| − | = | + | <source lang="bash"> |
| + | python setup.py --osx-frameworks install | ||
| + | </source> | ||
| − | === | + | === Install APBS with Fink === |
| − | + | 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]. | |
| − | |||
| − | |||
| − | + | 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]] | ||
| + | * [[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]] | ||
| − | + | [[Category:Installation|Mac]] | |
| + | [[Category:Nucleic_Acids|MAC Install]] | ||
| + | [[Category:Technical Issues|MAC Install]] | ||
| + | [[Category:Mac|MAC Install]] | ||
Latest revision as of 04:22, 12 November 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:
- 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.
./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
- 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