Cryo-EM structure solution with Phenix

Click on boxes in the figure to read an overview of each step.

GUI documentation for most-used programs:

• Automated structure determination using AlphaFold models with PredictAndBuild
• Assess the quality of your map with Mtriage
• Sharpen a map with AutoSharpen
• 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
• Optimize a map with local anisotropic sharpening

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