PHENIX is a comprehensive Python-based system for macromolecular structure solution, designed to automate all procedures in macromolecular X-ray crystallography. It integrates interpreted and compiled software modules, using Python for scripting and C++ for performance-critical tasks. The system includes a graphical user interface (GUI) that provides access to a wide range of tools for data analysis, model building, ligand fitting, and refinement. PHENIX supports both experimental phasing (MAD, SAD, MIR) and molecular replacement, with automated workflows for structure solution, model building, and refinement. It includes tools for substructure determination, phasing, noncrystallographic symmetry (NCS) analysis, and nucleic acid modeling. The system also provides validation tools for assessing model quality, including checks for covalent geometry, stereochemistry, and model-data fit. PHENIX is tightly integrated with other components, enabling seamless structure solution, building, and refinement. It supports a wide range of data formats and includes tools for generating and analyzing maps, as well as for refining atomic models. The system is designed for high-throughput and automated processing, with a focus on minimizing user intervention and maximizing the accuracy and efficiency of structure determination. PHENIX is widely used in the structural biology community for its robustness, flexibility, and integration with other tools like Coot and PyMOL.PHENIX is a comprehensive Python-based system for macromolecular structure solution, designed to automate all procedures in macromolecular X-ray crystallography. It integrates interpreted and compiled software modules, using Python for scripting and C++ for performance-critical tasks. The system includes a graphical user interface (GUI) that provides access to a wide range of tools for data analysis, model building, ligand fitting, and refinement. PHENIX supports both experimental phasing (MAD, SAD, MIR) and molecular replacement, with automated workflows for structure solution, model building, and refinement. It includes tools for substructure determination, phasing, noncrystallographic symmetry (NCS) analysis, and nucleic acid modeling. The system also provides validation tools for assessing model quality, including checks for covalent geometry, stereochemistry, and model-data fit. PHENIX is tightly integrated with other components, enabling seamless structure solution, building, and refinement. It supports a wide range of data formats and includes tools for generating and analyzing maps, as well as for refining atomic models. The system is designed for high-throughput and automated processing, with a focus on minimizing user intervention and maximizing the accuracy and efficiency of structure determination. PHENIX is widely used in the structural biology community for its robustness, flexibility, and integration with other tools like Coot and PyMOL.