Download PyMOL for Windows to view, animate and render 3D chemical structures. Its PyMOL is a free Open Source molecular viewing engine, rendering tool, and editor that can. PyMOL Other software can be installed upon request. MAC (running OS X) MS Office Adobe Suite PyMOL Other software can be installed upon request. Linux Protein Data Bank (Database of 3-dimensional structures of proteins and nucleic acids) CCP4 (Software for Macromolecular Crystallography) Phenix (Crystallographic refinement software).

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Created by Scientists for Scientists

Contemporary science is collaborative. To help scientists from different disciplines seamlessly work together, PyMOL interprets over 30 different file formats and its own format is supported on Windows, Mac, Linux, and iPad. With AxPyMOL users can insert fully interactive molecular data into their presentations making it easy to share results and concepts that a simple 2D figure cannot. Affirming its high-regard among scientists, PyMOL-generated images have graced countless covers of top-tier journals.

Create 3D Images and Movies with Ease

Complex visualization tasks that previously required expert knowledge now only require a few mouse clicks. PyMOL's straightforward graphical user interface allows first-time and expert users alike to create stunning 3D visualizations from their favorite file formats. Users can quickly and easily create movies that fly through a molecular landscape, elegantly depict protein structure morphing, and animate ensembles and trajectories.

First Class Support, First Class Community

The PyMOL support team offers technical support, printed tutorials, and screencasts for commercial users. For those who prefer to learn from an expert instead, classroom-style training is available worldwide. PyMOL also has over 100,000 active users with community-sponsored support available on the popular PyMOLWiki and pymol-users email list.

Citations and Acknowledgements

For instructions on citing PyMOL, please visit www.pymol.org/citing.

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.

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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

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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

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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

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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.

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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: