This page describes how to install PyMOL on Mac OS X.
1Incentive PyMOL
2Open-Source PyMOL
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Oct 19, 2016 Mac OS X Lion Free Download. October 19, 2016 March 8, 2017 Muhammad. Mac OS X Lion is a seventh powerful and major release of Mac OS X. It is a standalone Bootable DVD DMG Image installer of Lion OS X. Mac OSX Lion Overview. Apple has introduced many operating systems, Mac OS X is one of the powerful and stable releases from Apple. Since Mac Lion is introduced, it is continuously. This page was last modified on 28 June 2012, at 05:52. This page has been accessed 51,915 times. Content is available under GNU Free Documentation License 1.2. Feb 18, 2020 PyMOL for Mac OS X PyMOL is a comprehensive and powerful application that allows you to design and then visualize molecular structures. It enables the 3D visualization of all kinds of proteins and molecules, together with their related trajectories and surfaces.
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
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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.
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).
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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.
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.
Retrieved from 'http://pymolwiki.org/index.php?title=MAC_Install&oldid=12800'
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Mac OS X Lion 10.7 Features
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Better touch gestures.
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Technical name of macOS Leopard ISO file: macOS_10.7_lion.iso
Technical name of macOS Leopard DMG file: macOS_10.7_lion.dmg
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Mac OS X Lion ISO and DMG Installation Process
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For ISO Files:
Download the 7-Zip Extractor
Downloading the Windows ISO files.
Unzip and extract these ISO files
Burn the extracted files onto a bootable device (generally a DVD) which you can use for installation
For DMG Files:
Double click the DMG to make its content available (name will show up in the Finder sidebar), usually a window opens showing the content as well.
Drag the application from the DMG window into /Applications to install (may need an administrator password)
Wait for the copy process to finish.
Initiate the Installation process.
Sounds simple, right? Well, honestly, that’s all that had to be done. Now let’s move further.
macOS X Lion 10.7 Demo Video
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Mission Control – Expose, full screen apps, Dashboard, Spaces all in one
Auto-save
Auto resume app state when launched
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Well, we hope we could help you end your search. Thanks for reading. Stay in touch for more such content.