PyMOL Installation

The installation procedures for PyMOL are different for Linux and macOS. However, you can also refer to PyMOL offical website.

Linux

The easiest way is to use your distribution package manager.

$ sudo apt install pymol

Note: PyMOL version varies according to your distribution version.

Or, you can install PyMOL through Anaconda package management system.

PyMOL v1.8.x

An open source version of PyMOL v1.8.x is available from Anaconda. However, a conda environment must have Python 2 installed.

Follow these steps:

1. Create a new environment and activate it:

$ conda create --name pymol1.8 python=2.7
$ conda activate pymol1.8

2. Install PyMOL v1.8.x via Anaconda Cloud:

$ conda install -c mw pymol

3. Try PyMOL v1.8.x:

$ pymol

PyMOL v2.x

A version of PyMOL v2.x is available from Anaconda. However, a conda environment must have Python 3 installed.

Follow these steps:

1. Create a new environment and activate it:

$ conda create --name pymol2 python=3.7
$ conda activate pymol2

2. Install PyMOL v2.x via Anaconda Cloud:

$ conda install -c schrodinger pymol

3. Try PyMOL v2.x:

$ pymol

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macOS

An XQuartz installer is provided here.

PyMOL v1.8.x

An open source version of PyMOL v1.8.x is available from Anaconda. However, a conda environment must have Python 2 installed.

Follow these steps:

1. Create a new environment and activate it:

$ conda create --name pymol1.8 python=2.7
$ conda activate pymol1.8

2. Install PyMOL v1.8.x via Anaconda Cloud:

$ conda install -c mw pymol

3. Try PyMOL v1.8.x:

$ pymol

PyMOL v2.x

A version of PyMOL v2.x is available from Anaconda. However, a conda environment must have Python 3 installed.

Follow these steps:

1. Create a new environment and activate it:

$ conda create --name pymol2 python=3.7
$ conda activate pymol2

2. Install PyMOL v2.x via Anaconda Cloud:

$ conda install -c schrodinger pymol

3. Try PyMOL v2.x:

$ pymol

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If the options above does not work, you can try an installation via Homebrew package manager. A brief description of how to install open source PyMOL for macOS is provided here.

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