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Step-by-step guide

  1. Install XCode from App Store

  2. Start Terminal and install XCode Command Line Tools:
    sudo xcode-select --install

  3. You need MacPorts now.
    (https://www.macports.org/ (Need XCode)) download and install it.

  4. In Terminal again, execute:
    sudo port install tcl -corefoundation
    sudo port install tk -quartz
    sudo port install pymol

  5. Start PyMOL in terminal with:
    /opt/local/bin/pymol
  6. Done