Phenix Video Tutorials

The Phenix video tutorials explain how to run Phenix programs and how to interpret the results. All tutorial videos are available on the Phenix tutorials YouTube channel: www.youtube.com/c/phenixtutorials.

A list of all videos is also below (click on the panels to expand the view).

Tools for Cryo-EM

Overview

Overview of cryo-EM tools in Phenix

Map-tools

	Automated map sharpening with phenix.autosharpen
	Density modification for cryo-EM maps
	Automatic map interpretation with map_to_model

Refinement

How to run real_space_refine

Tools for X-ray crystallography

Reflection data

	Simulate a SAD experiment with phenix.plan_sad_experiment
	Scaling and merging anomalous data

Data analysis

	Checking data quality with phenix.xtriage
	Advanced Tutorial Xtriage - translational NCS (tNCS)
	Advanced Tutorial Xtriage - Checking for twinning
	Advanced Tutorial Xtriage - Space Group Identification, Ice rings & Wilson Plot

Molecular replacement

How to run Phaser-MR

Experimental Phasing

SAD phasing using AutoSol

Model Building

Automated model building with Phenix AutoBuild

Refinement

How to run phenix.refine

Other tools

	How to run Structure Comparison
	Fitting ligands into density with phenix.ligandfit
	Calculating polder maps

Other tutorials (apply to both cryo-EM and Xtallography)

Ligands

Basic Phenix eLBOW tutorial

Validation

	How to run MolProbity - step by step (web interface and Phenix GUI)
	MolProbity: All atom contacts tutorial

Mixed Tools

	How to use multiple refinement strategies and apply them to selected parts of a model
	How to use secondary structure restraints
	How to run PDB tools
	Changing custom parameters in phenix.refine
	Explaining the atom selection syntax

Lectures

Mini-lectures

Mini-lecture: Density modification

Other

Introduction to interactive low-resolution model building with ISOLDE

Full length lectures (45 min - 1 hour)

	SBGrid: Density Modification and Model Building with cryo-EM maps (T. Terwilliger)
	SBGrid: Atomic model refinement and validation in Phenix (P. Afonine)
	SBGrid: Map Sharpening; Model Building; other cryo-EM tools in Phenix (D. Liebschner)
	CCP4 Study weekend 2020: Cryo-EM map density modification and model-building (T. Terwilliger)
	CCP4 Study weekend 2020; EM Model Refinement (D. Liebschner)
	SBGrid: Atomic model, map and model-to-map fit validation (P. Afonine)
	Experimental Phasing (T. Terwilliger)
	Molecular Replacement in Phenix (P. Adams)
	Structure Refinement in Phenix (P. Afonine)
	Structure Validation with Phenix (P. Adams)
	Model-building using cryo-EM and crystallographic maps (T. Terwilliger)