PHENIX is a comprehensive Python-based system designed for macromolecular structure solution, emphasizing automation to streamline the process. It integrates interpreted and compiled software modules, leveraging Python for scripting and C/C++ for performance-critical tasks. PHENIX offers a graphical user interface (GUI) for improved user interaction and data visualization, and includes tools for analyzing X-ray diffraction data, substructure determination, phasing, noncrystallographic symmetry (NCS) detection, model building, ligand fitting, and structure refinement. The system supports various data formats and provides robust validation tools to ensure the quality of the resulting atomic models. PHENIX's automated procedures, such as experimental phasing and molecular replacement, significantly reduce the time and effort required for structure solution, making it accessible to a broader range of scientists.PHENIX is a comprehensive Python-based system designed for macromolecular structure solution, emphasizing automation to streamline the process. It integrates interpreted and compiled software modules, leveraging Python for scripting and C/C++ for performance-critical tasks. PHENIX offers a graphical user interface (GUI) for improved user interaction and data visualization, and includes tools for analyzing X-ray diffraction data, substructure determination, phasing, noncrystallographic symmetry (NCS) detection, model building, ligand fitting, and structure refinement. The system supports various data formats and provides robust validation tools to ensure the quality of the resulting atomic models. PHENIX's automated procedures, such as experimental phasing and molecular replacement, significantly reduce the time and effort required for structure solution, making it accessible to a broader range of scientists.