Phenix is a comprehensive software package for macromolecular structure determination that handles data from diffraction (X-ray, neutron and electron) and electron cryo-microscopy. Tasks include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Developers emphasize automation to minimize repetitive and time-consuming manual tasks. The graphical user interface streamlines the transition between programs, project tracking and re-running of previous tasks.