Phenix Video Tutorials

The Phenix video tutorials explain how to run Phenix programs and explain 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).

Overview

cryoem image Overview of cryo-EM tools in Phenix

Map-tools

Automated map sharpening with phenix.autosharpen
Automatic map interpretation with map_to_model

Refinement

phenix.real_space_refine How to run real_space_refine

Reflection data

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

Data analysis

xtriage image Checking data quality with phenix.xtriage
xtriage2 image Advanced Tutorial Xtriage - translational NCS (tNCS)
xtriage3 image Advanced Tutorial Xtriage - Checking for twinning
xtriage4 image Advanced Tutorial Xtriage - Space Group Identification, Ice rings & Wilson Plot

Molecular replacement

How to run Phaser-MR

Experimental Phasing

SAD phasing using AutoSol
phenix.refine Automated model building with Phenix AutoBuild

Refinement

phenix.refine How to run phenix.refine

Other tools

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

Ligands

elbow 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 run PDB tools
Changing custom parameters in phenix.refine
Explaining the atom selection syntax

Mini-lectures

Mini-lecture: Density modification

Other

Introduction to interactive low-resolution model building with ISOLDE

Full length lectures (45 min - 1 hour)

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)