mx cryo-em computational software-dev phenix-community
Info
PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is a multi-institutional software consortium developing the dominant automated macromolecular structure determination suite for X-ray crystallography, neutron diffraction, and cryo-EM. The consortium has been led by Paul Adams at LBNL since 1999, with partner sites at the University of Cambridge (Phaser), Duke University (MolProbity / Richardson Lab), Los Alamos National Laboratory / New Mexico Consortium, and UTHealth Houston. A 2021 Berkeley Lab Tech Transfer Award recognized the LBNL core team.
Why PHENIX matters for this landscape
PHENIX is built on the Computational Crystallography Toolbox (cctbx), which is the shared numerical foundation with DIALS (data processing). The consortium is the single largest concentration of current-generation structural biology software development in the US, and its training lineage runs back through CNS/XPLOR to Axel T. Brunger at Stanford University.
Current team (2026)
Lawrence Berkeley National Laboratory
| Member | Role |
|---|---|
| Paul Adams | Principal Investigator and Phenix Program Director |
| Pavel Afonine | Scientist - phenix.refine lead |
| Dorothee Liebschner | Scientist - real-space refinement, cryo-EM, validation |
| Nigel Moriarty | Scientist - eLBOW, ligand restraints |
| Billy Poon | Scientist - cctbx, build infrastructure |
| Oleg Sobolev | Scientist - refinement, riding hydrogen model |
| Peter H. Zwart | Scientist - cctbx, SAXS (also ALS beamline scientist) |
| Christopher Schlicksup | Postdoctoral Associate |
University of Cambridge (CIMR)
| Member | Role |
|---|---|
| Randy Read | Principal Investigator, Professor of Protein Crystallography; IUCr President |
| Airlie McCoy | Principal Research Associate; Phaser lead developer (2000-) |
| Alisia Fadini | Research Associate |
Duke University (Richardson Lab)
| Member | Role |
|---|---|
| Jane S. Richardson | Principal Investigator; MolProbity co-founder |
| Vincent Chen | Senior Research Associate; MolProbity / KiNG / Probe |
| Christopher Williams | Postdoctoral Associate; Reduce / CaBLAM |
| W. Bryan Arendall, III | Richardson Lab staff; XVTF |
Los Alamos National Laboratory / New Mexico Consortium
| Member | Role |
|---|---|
| Thomas Terwilliger | Laboratory Fellow and Senior Scientist; SOLVE/RESOLVE; PHENIX co-founder |
| Li-Wei Hung | Staff Member; LANL PHENIX contingent |
UTHealth Houston
| Member | Role |
|---|---|
| Matt Baker | Assistant Professor; cryo-EM tools integration |
Generational structure
PHENIX is a good illustration of the founder-to-current-generation handoff in macromolecular software:
| Role | Founders (1999-2010) | Current generation (2020s) |
|---|---|---|
| LBNL lead | Paul Adams | Paul Adams (continuing), with Pavel Afonine, Dorothee Liebschner, Billy Poon as senior scientists |
| Molecular replacement | Randy Read | Airlie McCoy (lead developer); Alisia Fadini |
| Validation (Duke) | Jane S. Richardson / David Richardson | Vincent Chen, Christopher Williams |
| Experimental phasing (LANL) | Thomas Terwilliger | Li-Wei Hung |
| Cryo-EM integration | (none originally) | Matt Baker (UTHealth), Dorothee Liebschner (LBNL) |
Software lineage context
The PHENIX codebase descends from CNS (Crystallography and NMR System) which Paul Adams helped develop as a postdoc in Axel T. Brunger’s lab at Yale. CNS in turn descended from XPLOR (also Brunger). Parallel descendants from the same root include XPLOR-NIH (Charles Schwieters, Marius Clore). This means PHENIX and XPLOR-NIH are computational siblings with shared DNA in the Brunger lineage.
Key Relationships
- CCP4 — European parallel consortium for MX software; Phaser is co-distributed via both
- DIALS — data processing partner built on the same cctbx foundation
- MolProbity — validation pipeline, shared Duke origin
- wwPDB — PHENIX is embedded in OneDep deposition/validation
- ALS — LBNL home facility; Berkeley Center for Structural Biology
- NIAC (Aaron Brewster, Chair) — data format governance partner at LBNL
Funding
- NIH P01 GM063210 (to Paul Adams, Randy Read, Jane S. Richardson) — core multi-institutional program project grant
- NIH R01/R24 supplements
- 2017 NIH $9.3M award for further PHENIX development
- DOE support via LBNL
Primary sources
- PHENIX team page: https://phenix-online.org/people
- 2021 Berkeley Lab Tech Transfer Award (Phenix Team): https://recognition.lbl.gov/2021-laureates/
- Liebschner et al., “Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix” (Acta Cryst D 2019): https://pubmed.ncbi.nlm.nih.gov/31588918/