Python-based
Hierarchical
ENvironment
for
Integrated
Xtallography
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).
PHENIX builds upon Python, the Boost.Python Library, and C++ to provide an environment for automation and scientific computing. Many of the fundamental crystallographic building blocks, such as data objects and tools for their manipulation are provided by the Computational Crystallography Toolbox (cctbx). The computational tasks which perform complex crystallographic calculations are then built on top of this. Finally, there are a number of different user interfaces available in PHENIX. In order to facilitate automated operation there is the Project Data Storage (PDS) that is used to store and track the results of calculations.
The PHENIX development team consists of members from Lawrence Berkeley Laboratory (Paul Adams's group), Los Alamos National Laboratory (Tom Terwilliger's group), Cambridge University (Randy Read's group) and Duke University (the Richardsons' group). Researchers from Texas A&M University (Tom Ioerger's and Jim Sacchettini's groups) participated in the first five years of PHENIX development.
The development of PHENIX is funded by the National Institutes of Health (General Medicine) under grant P01GM063210, and the PHENIX Industrial Consortium.
Citing PHENIX
If you use PHENIX to solve a structure please cite this publication:
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. D. Liebschner, P. V. Afonine, M. L. Baker, G. Bunkóczi, V. B. Chen, T. I. Croll, B. Hintze, L.-W. Hung, S. Jain, A. J. McCoy, N. W. Moriarty, R. D. Oeffner, B. K. Poon, M. G. Prisant, R. J. Read, J. S. Richardson, D. C. Richardson, M. D. Sammito, O. V. Sobolev, D. H. Stockwell, T. C. Terwilliger, A. G. Urzhumtsev, L. L. Videau, C. J. Williams and P. D. Adams. Acta Cryst. (2019). D75, 861-877
Publications
A number of publications describing PHENIX can be found at: