Videos and slides from Phenix user workshops
Video recordings and/or slides from Phenix user workshops.
General information
- All videos are available on the Phenix tutorials YouTube channel: www.youtube.com/c/phenixtutorials.
- Tutorials with example data are described here.
Future user workshops
No user workshop is currently scheduled.
Past user workshops
- Introduction to Phenix (Pavel Afonine) (pdf)
- Data analysis with Xtriage (Pavel Afonine) (pdf)
- Using AlphaFold predictions for structure determination (Oleg Sobolev) (pdf)
- Experimental phasing (Pavel Afonine) (pdf)
- Molecular Replacement (Oleg Sobolev) (pdf)
- Refinement (Pavel Afonine) (Model Refinement) (Refinement X-ray vs cryo-EM) (AQuaRef)
- Ligands (Oleg Sobolev) (pdf)
- Model validation (Pavel Afonine) (pdf)
- Advanced low-resolution refinement (Oleg Sobolev) (pdf)
- Introduction to Phenix (Dorothee Liebschner) (pdf)
- Using AlphaFold predictions for structure determination (Tom Terwilliger) (pdf) (video)
- MR/Docking (Randy Read) (pdf) (video)
- Ligands (Nigel Moriarty) (pdf) (video)
- Refinement Xray and cryo-EM (Pavel Afonine) (pdf) (video)
- Advanced Restraints (Oleg Sobolev) (pdf)
- MolProbity Validation (Christopher Williams) (pdf) (video)
- Introduction to Phenix (Dorothee Liebschner) (pdf)
- Phenix tools for crystallography (Dorothee Liebschner) (pdf)
- Diffraction Data Analysis (Xtriage) (Pavel Afonine) (pdf)
- Using AlphaFold predictions for structure determination (Christopher Williams) (pdf)
- SAD phasing in Phenix (Dorothee Liebschner) (pdf)
- Refinement X-ray (Pavel Afonine) (pdf)
- MolProbity Validation (Christopher Williams) (pdf)
- Ligands (Nigel Moriarty) (pdf)
- cryo-EM tools in Phenix (Pavel Afonine) (pdf)
- Refinement cryo-EM (Pavel Afonine) (pdf)
- Advanced Restraints (Oleg Sobolev) (pdf)
- PDB tools tutorial (Christopher Williams) (pdf)
- PDB deposition (Oleg Sobolev) (pdf)
- Introduction to Phenix (Oleg Sobolev) (pdf)
- Diffraction Data Analysis (Xtriage) (Pavel Afonine) (pdf)
- Using AlphaFold predictions for structure determination (Christopher Williams) (pdf)
- Molecular Replacement (Dorothee Liebschner) (pdf)
- Refinement X-ray (Pavel Afonine) (pdf)
- MolProbity Validation (Christopher Williams) (pdf)
- Ligands (Nigel Moriarty) (pdf)
- Steps in cryo-EM (Pavel Afonine) (pdf)
- Validation cryo-EM (Pavel Afonine) (pdf)
- Refinement cryo-EM (Pavel Afonine) (pdf)
- Advanced Restraints (Oleg Sobolev) (pdf)
- Introduction to Phenix (Nigel Moriarty) (pdf)
- Data Validation (Pavel Afonine) (pdf)
- Using AlphaFold Models (Christopher Williams) (pdf)
- Molecular Replacement (Dorothee Liebschner) (pdf)
- Refinement (Pavel Afonine) (pdf)
- MolProbity Validation (Christopher Williams) (pdf)
- ChimeraX (Zach Pearson) (pdf)
- Ligands (Nigel Moriarty) (pdf)
- Introduction to Phenix (Dorothee Liebschner) (pdf)
- Xtriage (Dorothee Liebschner) (pdf)
- Refinement (Pavel Afonine) (pdf)
- Molecular Replacement (Dorothee Liebschner) (pdf)
- Using AlphaFold predictions for structure determination (Tom Terwilliger) (pdf)
- Ligands (Dorothee Liebschner) (pdf)
- Experimental Phasing (Tom Terwilliger) (pdf)
- MolProbity Validation (Christopher Williams) (pdf)
- Introduction to Phenix (Dorothee Liebschner) (pdf)
- Using AlphaFold predictions for structure determination (Tom Terwilliger) (pptx)
- Molecular Replacement (Airlie McCoy) (pdf)
- Docking (Randy Read) (pdf)
- Density modification in Crystallography and cryo-EM (Tom Terwilliger) (pptx)
- Refinement (Oleg Sobolev) (pdf)
- Validation (Christopher Williams) (pdf)
- Introduction to Phenix (Dorothee Liebschner) (pdf)
- Strategy for X-ray or Cryo-EM structure determination using AlphaFold models (Tom Terwilliger) (pdf)
- Evaluating X-ray data with Xtriage (Dorothee Liebschner) (pdf)
- Xray refinement (Pavel Afonine) (pdf)
- Ligands (Dorothee Liebschner) (pdf)
- Cryo-EM Data evaluation with Mtriage (Pavel Afonine) (pdf)
- Cryo-EM refinement (Pavel Afonine) (pdf)
04/07/2021
- Introduction to Phenix (Paul Adams) (video)
- Cryo-EM map improvement (Tom Terwilliger) (video)
- Automated model building (Tom Terwilliger) (video)
- Zoom chat transcript
- Real Space Refinement (Pavel Afonine) (video)
- Restraints in Phenix (Nigel Moriarty) (video)
- Model validation (Jane Richardson) (video)
- Zoom chat transcript
11/17/2020
- Introduction to Phenix (Paul Adams) (video)
- Experimental Phasing and model building (Tom Terwilliger) (video)
- Top tips for molecular replacement (Phaser team) (video)
- Q&A session (video)
- Zoom chat transcript
- Refinement (Pavel Afonine) (video)
- Ligands and restraints (Nigel Moriarty) (video)
- Model validation (Christopher Williams) (video)
- Q&A session (video)
- Zoom chat transcript
9/15/2020
- Introduction to Phenix (Paul Adams) (video)
- Cryo-EM map improvement (Tom Terwilliger) (video) (slides)
- Automated model Building (Tom Terwilliger) (video) (slides)
- Q&A session (video)
- Zoom chat transcript
- Refinement with phenix.real_space_refine (Pavel Afonine) (video)
- Ligands and restraints (Nigel Moriarty) (video)
- Validation (Jane Richardson) (video)
- Q&A session (video)
- Zoom chat transcript