Molecule Tutorials - Herong's Tutorial Examples - v1.21, by Dr. Herong Yang
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.
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