3D rendering of CD1d, a protein expressed on the surface of various human antigen-presenting cells. Involved in the presentation of lipid antigens to T cells.

Structural Biology Workshop

Phenix Software Suite for Protein Crystallography & cryo-EM

Thursday, Nov. 9 – Friday, Nov. 10, 2023
University of Kansas, School of Pharmacy
1020 Becker Drive, Lawrence, KS

The workshop will feature software developers from the Phenix Consortium who manage the software suite Phenix (Python-based Hierarchical ENvironment for Integrated Xtallography) for automated determination of molecular structures using X-ray crystallography and cryo-EM. The PHENIX suite is a complete software package used by structural biologists to analyze crystallographic (X-ray, neutron and electron) and cryo-EM data.


Phenix developers will provide lectures on the background and theory behind the software.

Hands-on Sessions

Hands-on sessions will provide all participants an opportunity to learn and utilize the various tools within Phenix related to structural biology. The workshop is open to students, postdocs and PIs of all structural biology skill levels. Attendees new to the structural biology field will learn the methods used for structure solution, refinement and analysis during a tutorial session hosted by the Phenix team. Experienced structural biologists are encouraged to bring their own data, particularly problematic data sets, for analysis.


Attendees should bring a personal laptop with the Phenix software package and the Coot graphics software installed. The software is free to academics and nonprofits.


Please contact Kymbre Dwyer at kymbre.dwyer@ku.edu or 785-864-7026.

Detailed workshop schedule


Thursday, Nov. 9 | KU School of Pharmacy, Room 3002

Instructors: Pavel Afonine, Dorothee Liebschner, Nigel Moriarty, Zach Pearson and Christopher Williams

Schedule for Thursday, Nov. 9
7:30 a.m.Check-in + continental breakfast (atrium) 
8:30 a.m.Welcome + introduction to PhenixSL / NM
9:30 a.m.Data analysis (lecture)PA
10 a.m.BREAK 
10:15 a.m.Alphafold (lecture)CW
10:30 a.m.Alphafold prediction tutorialDL
10:40 a.m.MR (lecture + tutorial)DL
11:10 a.m.Experimental phasing (lecture + tutorial)DL
11:40 a.m.Refinement I (lecture)PA
12:30 p.m.LUNCH (Mortar & Pestle Cafe, first floor) 
1:30 p.m.Refinement II (tutorial)PA
2:30 p.m.BREAK 
2:45 p.m.Model validation (lecture + tutorial)CW
4 p.m.ChimeraX (lecture + tutorial)ZP
5:30 p.m.END 


Friday, Nov. 10 | KU School of Pharmacy, Room 2020

Please note that these sessions are in a different room than the previous day.

Schedule for Friday, Nov. 10
7:30 a.m.Continental breakfast 
8:30 a.m.Ligands (lecture + tutorial)NM
10 a.m.BREAK 
10:15 a.m.1:1 sessions with Phenix teamAll
12:30 p.m.END 


Sponsored by the Protein Structure & X-ray Crystallography Laboratory and the Center of Biomedical Research Excellence: Chemical Biology of Infectious Disease at the University of Kansas, with support from the KU Office of Research