Software

Phenix

Phenix (Python-based Hierarchical ENvironment for Integrated Xtallography) is a comprehensive system for macromolecular structure determination using X-ray crystallography, cryo-electron microscopy, and neutron diffraction. Phenix includes automated tools for experimental phasing, molecular replacement, model building, refinement, validation, and ligand fitting.

Recent Phenix developments include integration of AlphaFold predictions into experimental structure determination, density modification of cryo-EM maps, automated model building from cryo-EM maps, and map improvement tools.

Visit phenix-online.org

SOLVE & RESOLVE

SOLVE and RESOLVE were developed by Tom Terwilliger at Los Alamos National Laboratory beginning in the mid-1990s. Together they formed a complete pipeline for macromolecular crystal structure determination — from experimental phasing through density modification and automated model building.

SOLVE was the first fully automated software for macromolecular structure analysis using experimental phasing. It introduced probabilistic approaches to heavy-atom parameter estimation, correlated phasing of multiple isomorphous replacement and anomalous diffraction datasets, and automated decision-making in structure solution. SOLVE supported MAD, SAD, MIR, and SIR methods, making experimental phasing accessible to non-specialist users.

RESOLVE was the first likelihood-based system for density modification and one of the early automated model building tools. It introduced maximum-likelihood density modification, automated model building by template matching and iterative fragment extension, and prime-and-switch phasing to reduce model bias. RESOLVE could automatically build and refine protein models starting from experimental electron density maps.

The methods in SOLVE and RESOLVE have been incorporated into the Phenix software suite, where they continue to be developed and extended. The Phenix AutoSol wizard is essentially the next generation of the SOLVE and RESOLVE algorithms for automated experimental phasing, density modification, and model building. SOLVE and RESOLVE can still be run as standalone programs for users who prefer the original interfaces.

SOLVE/RESOLVE Archival Documentation (PDF)