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.
Presentations
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.
Software
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.
Questions
Please contact Kymbre Dwyer at kymbre.dwyer@ku.edu or 785-864-7026.
Register online
The workshop is open to students, postdocs and PIs of all structural biology skill levels. The $50 registration fee covers programming, breakfast/lunch on Thursday and breakfast on Friday.
Detailed workshop schedule
Thursday, Nov. 9 | KU School of Pharmacy, Room 3002
Instructors: Pavel Afonine, Dorothee Liebschner, Nigel Moriarty, Zach Pearson and Christopher Williams
| Time | Session | Instructor |
|---|---|---|
| 7:30 a.m. | Check-in + continental breakfast (atrium) | |
| 8:30 a.m. | Welcome + introduction to Phenix | SL / 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 tutorial | DL |
| 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.
| Time | Session | Instructor |
|---|---|---|
| 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 team | All |
| 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