Install Open Source PyMol with Homedrew

This section provides a tutorial on how to install open source PyMol using Homebrew package manager. Installation failed because Xcode.app is required.

If you want to install the open source edition of PyMol using Homebrew package manager. you can try these steps:

1. Go to Homebrew Website at brew.sh. It will tell you to run the following command on your macOS:

/usr/bin/ruby -e "$(curl\
  -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

==> You are using macOS 10.12.
==> We (and Apple) do not provide support for this old version.
This installation may not succeed.
...
/usr/local/bin/brew
/usr/local/share/doc/homebrew
/usr/local/share/man/man1/brew.1
/usr/local/share/zsh/site-functions/_brew
/usr/local/etc/bash_completion.d/brew
/usr/local/Homebrew
...
==> Downloading and installing Homebrew...
remote: Enumerating objects: 47, done.
remote: Counting objects: 100% (47/47), done.
remote: Compressing objects: 100% (43/43), done.
remote: Total 129532 (delta 22), reused 9 (delta 4), pack-reused 129485
Receiving objects: 100% (129532/129532), 30.92 MiB | 37.00 KiB/s, done.
Resolving deltas: 100% (95053/95053), done.
From https://github.com/Homebrew/brew
 * [new branch]          master     -> origin/master
...
remote: Enumerating objects: 5099, done.
remote: Counting objects: 100% (5099/5099), done.
remote: Compressing objects: 100% (4895/4895), done.
remote: Total 5099 (delta 50), reused 315 (delta 8), pack-reused 0
Receiving objects: 100% (5099/5099), 4.14 MiB | 7.00 KiB/s, done.
Resolving deltas: 100% (50/50), done.
Tapped 2 commands and 4881 formulae (5,140 files, 12.8MB).
Already up-to-date.
==> Installation successful!
...

2. Homebrew installed ok and ready to install Open Source PyMol:

herong$ brew install brewsci/bio/pymol

Updating Homebrew...
==> Tapping brewsci/bio
Cloning into '/usr/local/Homebrew/Library/Taps/brewsci/homebrew-bio'...
...
==> Installing pymol from brewsci/bio
freeglut: XQuartz 2.7.11 (or newer) is required to install this formula.
X11Requirement unsatisfied!
You can install with Homebrew Cask:
  brew cask install xquartz
...
qt: A full installation of Xcode.app is required to compile
this software. Installing just the Command Line Tools is not sufficient.]
Xcode can be installed from the App Store.
Error: Unsatisfied requirements failed this build.

3. Fix the XQuartz issue:

herong$ brew cask install xquartz

Cloning into '/usr/local/Homebrew/Library/Taps/homebrew/homebrew-cask'...
...
installer: Package name is XQuartz 2.7.11
installer: Installing at base path /
installer: The install was successful.
🍺  xquartz was successfully installed!

4. Xcode.app is still required. I will do it later.

Table of Contents

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 SDF (Structure Data File)

 RDKit: Open-Source Cheminformatics Software

PyMol Installation

 What Is PyMol

 Install PyMol Incentive Edition on macOS

 Install PyMol Open Source Edition

 Compile PyMol Source Code

Install Open Source PyMol with Homedrew

 Install Open Source PyMol with Fink

 PyMol GUI and CLI

 PyMol Selections

 PyMol Editing Functions

 PyMol Measurement Functions

 PyMol Movie Functions

 PyMol Python Integration

 PyMol Object Functions

 ChEMBL Database - European Molecular Biology Laboratory

 PubChem Database - National Library of Medicine

 PDB (Protein Data Bank)

 INSDC (International Nucleotide Sequence Database Collaboration)

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB