How To Install Run XQuartz X11 Applications On Mac OS X 10 10 Yosemite Or Later.Here is the link to download Xquartz (which is also X11): http://xquartz.maco. 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.
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This page describes how to install PyMOL on Mac OS X.
- 1Incentive PyMOL
- 2Open-Source PyMOL
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.
X11 Download For Mac
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: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.
You may need to make sure that the dependencies are installed with the required flags, e.g. for MacPorts:
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:
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
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.
X11 Mac Os X
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:
See Also
- Bill Scott’sMacOSX-specific .pymolrc file and his crystallographic software wiki and website, including instructions on how to install precompiled binary packages using fink.
X11 For Mac
