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PHENIX - Software for Computational Crystallography



  • Automated macromolecular crystallography


  • Requires little or no human intervention
  • Significantly decrease time required to solve a structure
  • Increase throughput of structure solutions
  • Users at all levels, from beginners to experts, can benefit from this software

PHENIX strategy interface showing graphical output. Left, a simple graph showing the Wilson plot, fitted line and parameters derived from the plot. Right, a graphical representation of a molecule imported in PHENIX for a molecular replacement translation search. Visualized from PHENIX using the PyMol program (written by Warren DeLano)



Researchers at Berkeley Lab and other institutions are seeking industrial partners to join a consortium to advance the development of PHENIX (Python-based Hierarchical EnviroNment for Integrated Xtallography) software for automated macromolecular crystallography. The basis for the software, the Python system, provides a powerful object-oriented scripting language.

This novel software is expected to permit all tasks required for the computation of phases, automated map interpretation, model building and refinement to be integrated with newly-developed procedures for automated decision-making. Eventually, PHENIX is expected to take X-ray diffraction data and rapidly produce minimally-biased atomic coordinates with little or no human intervention. At present, the need for continual, manual intervention makes rapid, minimally-biased structure solution extremely difficult. Human intervention is required to obtain initial phases for the electron density map, build the initial model, and complete the model with refinement. As a result, the time required to solve a structure after the data have been collected is often on the order of weeks or months. The PHENIX system is expected to significantly decrease this time and therefore provide a valuable tool to increase throughput for all crystallographers.

For expert users, a flexible interface to the broad array of methods available in PHENIX will facilitate the solution of even the most difficult crystallographic problems. Berkeley Lab’s new system for automated crystallography is being built on a strong foundation that can accommodate current plans and future developments. Researchers are developing a toolkit that will provide an environment for integrating crystallographic tasks and automated decision-making. A fundamental feature of the toolkit is that the entire history of the structure solution, along with all the structural information generated, will be stored in the Project History database. This design allows the various tasks involved in the structure solution process to communicate information exclusively via the database. Complicated interfaces for the communication between tasks are avoided and new ideas can be rapidly implemented and tested.

We are seeking industrial partners to join our existing industrial consortium to speed the development of the PHENIX software program. For technical information, please visit

For information on a software program for rapid in-house processing of x-ray diffraction images go to:

LABELIT – Software for Macromolecular Diffraction Data Processing, IB-1960


  • Available for collaboration



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