Structural biology is a field that uses various techniques, including X-ray diffraction, neutron diffraction, and electron cryo-microscopy (cryo-EM), to determine the three-dimensional structures of macromolecules. These structures are essential for understanding biological processes and developing new therapeutics. Phenix is a comprehensive software package that handles data from these techniques to determine macromolecular structures. Phenix includes tools for data-quality assessment, map improvement, model building, and validation. The software emphasizes automation to minimize repetitive tasks and encourages best practices. Phenix provides a graphical user interface for accessing its command-line features and streamlines the workflow between programs. X-ray diffraction relies on the interaction of X-rays with the electron cloud of atoms in a crystal. The phase information is lost during the diffraction experiment and must be inferred. Neutron diffraction, which uses the interaction of neutrons with atomic nuclei, provides direct atomic positions. Cryo-EM uses electrons to interact with the electrostatic field of atoms in a sample, allowing for the reconstruction of three-dimensional structures. Cryo-EM has improved significantly, with high-resolution structures now being determined routinely. Phenix is designed to handle data from X-ray, neutron, and cryo-EM techniques, with specific tools for each method. The software automates procedures to reduce manual tasks and provides user-friendly features for both novice and expert users. Recent developments in Phenix include tools for cryo-EM map analysis and improved structure-solution workflows. The software also includes tools for data-quality assessment, map optimization, model building, and refinement. These tools help in determining the best fit between the experimental data and the model. Phenix also supports neutron crystallography, with tools for adding H/D atoms and joint refinement against X-ray and neutron data. Validation tools in Phenix help identify problems in macromolecular models and guide corrections throughout the structure-solution process. The software provides comprehensive validation for crystallographic and cryo-EM data and models, ensuring high-quality results.Structural biology is a field that uses various techniques, including X-ray diffraction, neutron diffraction, and electron cryo-microscopy (cryo-EM), to determine the three-dimensional structures of macromolecules. These structures are essential for understanding biological processes and developing new therapeutics. Phenix is a comprehensive software package that handles data from these techniques to determine macromolecular structures. Phenix includes tools for data-quality assessment, map improvement, model building, and validation. The software emphasizes automation to minimize repetitive tasks and encourages best practices. Phenix provides a graphical user interface for accessing its command-line features and streamlines the workflow between programs. X-ray diffraction relies on the interaction of X-rays with the electron cloud of atoms in a crystal. The phase information is lost during the diffraction experiment and must be inferred. Neutron diffraction, which uses the interaction of neutrons with atomic nuclei, provides direct atomic positions. Cryo-EM uses electrons to interact with the electrostatic field of atoms in a sample, allowing for the reconstruction of three-dimensional structures. Cryo-EM has improved significantly, with high-resolution structures now being determined routinely. Phenix is designed to handle data from X-ray, neutron, and cryo-EM techniques, with specific tools for each method. The software automates procedures to reduce manual tasks and provides user-friendly features for both novice and expert users. Recent developments in Phenix include tools for cryo-EM map analysis and improved structure-solution workflows. The software also includes tools for data-quality assessment, map optimization, model building, and refinement. These tools help in determining the best fit between the experimental data and the model. Phenix also supports neutron crystallography, with tools for adding H/D atoms and joint refinement against X-ray and neutron data. Validation tools in Phenix help identify problems in macromolecular models and guide corrections throughout the structure-solution process. The software provides comprehensive validation for crystallographic and cryo-EM data and models, ensuring high-quality results.