PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.
The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template and pattern-based automated model-building (RESOLVE), automated macromolecular refinement (phenix.refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the command line.
There are also a number of tools in PHENIX for handling ligands. Automated fitting of ligands into the electron density is facilitated via the LigandFit wizard. Besides being able to fit a known ligand into a difference map, the LigandFit wizard is capable to identify ligands on the basis of the difference density only. Stereo chemical dictionaries of ligands whose chemical description is not available in the supplied monomer library for the use in restrained macromolecular refinement can be generated with the electronic ligand builder and optimization workbench (eLBOW).
All CHPC Software Documentation has been moved: https://www.chpc.utah.edu/
The main Phenix website can be found at http://www.phenix-online.org/
This includes a searchable database found: https://www.chpc.utah.edu/sys/pkg/phenix/phenix-1.9-1692/phenix_env
To use PHENIX, go to a work directory and type: