MAC Install: Difference between revisions

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:

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'

@@ Line 1: / Line 1: @@
-[[Category:Installation|Mac]]
+This page describes how to install PyMOL on Mac OS X.
-http://images.apple.com/powermac/images/solutionsscience20050427.jpg
-__TOC__
-=Installing MacPyMOL=
-http://delsci.com/macpymol/macpymol350.jpg
-===Essentials===
-The [http://delsci.com/macpymol/ download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling.  Most other mice will also work well.
-One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it.  These often mess with the mapping of the middle button or have other horrific side effects.  Fortunately, with OS X, you should not need to.
+== Incentive PyMOL ==
-I ([[User:Wgscott|Bill Scott]]) 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.
+[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.
-===Extras===
+Download: https://pymol.org/
-You don't need any of these to use MacPyMOL.  But you didn't really '''need''' a Mac either.  Face it: You need these.
+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).
-====Mighty Mouse====
+Uninstallation: Move '''/Applications/PyMOL.app''' to Trash
-http://images.apple.com/mightymouse/images/index360scroll220050802.gif
+=== Launching from Command Line ===
-A 3-button mouse is essential.  [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.
+The unix executable resides at '''/Applications/PyMOL.app/Contents/MacOS/PyMOL'''
-====PowerMate Dial====
+=== X11 Hybrid ===
-http://www.griffintechnology.com/images/products/prod_powermate_a.jpg
+''Applies to PyMOL 1.x, not to PyMOL 2.x''
-The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].
+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]].
-====Stereo====
+Requires [http://xquartz.macosforge.org/ XQuartz].
-http://images.apple.com/powermac/images/graphicspymol20051018.jpg
+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'''
-The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window].  There is more information in the [[Monitors Hardware Options]] section.
+=== 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>
-=Installing X-windows based pymol on Mac OS X=
+'''Source:''' [https://sourceforge.net/p/pymol/mailman/message/11671952/ Warren DeLano; PyMOL Users Archive]
-===Why would you want to do this?===
+== Open-Source PyMOL ==
-#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol
+=== Package managers ===
-#You just happen to prefer the [http://wiki.python.org/moin/TkInter 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.
-----
+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.
-===Simplest Installation===
+<source lang="bash">
+# Homebrew (recommended)
+brew install brewsci/bio/pymol
-====Install pymol with Fink====
+# Fink
-http://pdb.finkproject.org/img/mlogo.png
+fink install pymol-py27
-By far the simplest way to install the X-windows based version of pymol on OS X is by using the [http://fink.sourceforge.net/ fink package management system].  To compile it, all you need to do is issue the command
+# MacPorts
+sudo port install pymol
+</source>
- fink install pymol-py24
+You may need to make sure that the dependencies are installed with the required flags, e.g. for MacPorts:
-(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:
+<source lang="bash">
+# MacPorts
+sudo port install tcl -corefoundation
+sudo port install tk -quartz
+</source>
- sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.
+If PyMOL complains that it wasn't able to find X11, try starting xquartz first, then run pymol from the console.
-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
+=== 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).
-I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [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].
+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://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.
+<source lang="bash">
+python setup.py --osx-frameworks install
+</source>
-====Install APBS and friends with fink====
+=== 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 mpi version of apbs].
+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
@@ Line 81: / Line 83: @@
 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.
-'''Nucleic acids''' may prove problematic for the apbs plugin.  If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.
+=== 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'
-===Gratuitous Eye-Candy Tweaks===
+== See Also ==
-[[Image:snap_mac.png]]
-You can get the fink installed X-windows based pymol-py24 to use an aqua-based tkinter menu as follows:
+* [[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]]
-. Install a Framework build of Python2.4 as follows:
+[[Category:Installation|Mac]]
+[[Category:Nucleic_Acids|MAC Install]]
- mkdir src
+[[Category:Technical Issues|MAC Install]]
- cd src
+[[Category:Mac|MAC Install]]
- curl -O http://www.python.org/ftp/python/2.4.2/Python-2.4.2.tgz
- tar xvfz Python-2.4.2.tgz
- cd Python-2.4.2
- export PATH=/usr/bin:$PATH
- ./configure --enable-framework
- make
- sudo make frameworkinstall
-. Remove the following empty directory by issuing the command
- sudo rmdir /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages
-. Make a symbolic link to your fink site-packages directory:
-sudo ln -s /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages /sw/lib/python2.4/site-packages
-This enables your new framework python to use all of the extras, like pmw, that you installed as dependencies for pymol.
-. Edit the file /sw/bin/python, and change the line
- /sw/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"
-to
- /Library/Frameworks/Python.framework/Versions/Current/bin/python2.4  $PYMOL_PATH/modules/pymol/__init__.py "$@"
-.  Now issue
- /sw/bin/pymol
-and you should see something that looks like this full-size [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png screenshot of pymol with an aqua-tkinter pmw GUI] and X-windows based molecular display window. Also shown in this screenshot is the APBS plugin in action.