Workshop 2: X-ray and Cryo-EM structure determination with AlphaFold and Phenix

Date/Time: Friday, July 29, 2022 @ 8:00 AM PT
Portland Marriott Downtown, Portland, Oregon
Organizational Contact: Dorothee Liebschner



The workshop is on structure determination of biological macromolecules with the software package Phenix. The lectures and tutorials will cover key stages of structure solution: from obtaining initial atomic models given experimental data (diffraction intensities or a 3D reconstruction) to final complete, refined and validated structures. Considering cryo-EM and crystallography, the tutors will compare and contrast tools and methods available in Phenix to perform these tasks. Particular focus is on Phenix tools and methods that are designed for handling predicted models (e.g. AlphaFold) for X-ray crystallography and cryo-EM.

Attendees are encouraged to actively participate in the workshop by asking questions about the presentations and by following tutorial exercises. The sessions introduce the Phenix system and the core algorithms that it uses; lectures are followed by hands-on tutorials. The workshop will conclude with a survey and general discussion.



Dorothee Liebschner

Lawrence Berkeley National Lab

Pavel Afonine

Lawrence Berkeley National Lab

Billy Poon

Lawrence Berkeley National Lab

Thomas Terwilliger

Los Alamos National Lab, Senior Scientist, New Mexico Consortium




 TimeTopic Lecturer
8:00  Welcome: Introduction to Phenix, Introduction to the GUI, set up Phenix D. Liebschner/ B.Poon
8:45 Overview -- Strategy for X-ray or Cryo-EM structure determination using AlphaFold models (lecture 30 min) T. Terwilliger
9:15 Predicting your structure with AlphaFold and trimming it with ProcessPredictedModel (demo, 30 min) T. Terwilliger
9:45 Solving an X-ray structure automatically by MR with PredictAndBuild (demo with pre-computed data, 30 min) T. Terwilliger
10:15 Break  
10:45 Evaluating X-ray data with Xtriage D. Liebschner
11:00 Xray refinement (lecture, 30 min) P. Afonine
11:30 Xray refinement with AlphaFold reference models (demo, 30 min) P. Afonine
12:30 Lunch  
13:00 Ligands (lecture & demo, 30 min) D. Liebschner
13:30 Cryo-EM Data evaluation with Mtriage (short lecture & demo, 15 min) P. Afonine
13:45 Cryo-EM map manipulations, map improvement with LocalAnisoSharpen and ResolveCryoEM (demo, 45 min) T. Terwilliger
14:30 Break  
15:00 Automatic cryo-EM map interpretation with PredictAndBuild (demo with pre-computed data, 30 min) T. Terwilliger
15:30 Cryo-EM refinement (lecture and demo, 30 min) P. Afonine
16:00 Model validation (lecture & demo, 30 min) D. Liebschner
16:30 Q&A D. Liebschner
16:50 finish: workshop survey and wrap up D. Liebschner