Cryo-EM structure solution with Phenix

Click on boxes in the figure to read an overview of each step. Also see the AlphaFold models in Phenix overview and video tutorials for using AlphaFold models in Phenix. You can use the Phenix chatbot to get help on using any Phenix program. Just ask it any question about using Phenix.

GUI documentation for most-used programs:

• Predict a structure with AlphaFold using PredictModel
• Automated structure determination using AlphaFold models with PredictAndBuild
• Assess the quality of your map with Mtriage
• Optimize a map with MapSharpening
• Density modify a map with RESOLVE cryo-EM
• Identify symmetry in a map with Map-Symmetry
• Extract a box with map and model with Map-Box
• Dock a model into a map with Dock-in-map
• Flexibly fit a model to a map with CryoFit
• Build a model with Map-to-model
• Refine your model against a map with phenix.real_space_refine
• Generate geometry restraints
• Build ordered water with Douse
• Model heterogenicity by refinement against multiple maps phenix.varref
• Complete list of programs for each structure solution step

Other map tools:

• Calculate a local resolution map
• Combine best parts of focused maps
• Convert map to structure factors
• Segment a map

Other model building tools:

• Rapid model-building
• Guess sequences from map
• Compare CA/P in two models
• Adjust a CA/CB model
• Fix register errors