Video tutorials
Phenix programs and their functions
Running Phenix with the graphical interface
Tutorials and Examples
Dictionary of crystallographic and other terms
FAQs: Frequently asked questions
How to install, setup and run Phenix
Complete Phenix reference documentation
Find a program or regression test
Bibliography
Index
AlphaFold and Phenix
Running AlphaFold2 in Google CoLab
Process predicted model
Dock processed predicted model in cryo-EM map
Rebuild docked predicted model in cryo-EM map
Process, dock and rebuild predicted model in cryo-EM map
Trim parts of one model overlapping another
Phenix Documentation for X-ray Crystallography
Checking data quality | Experimental phasing | Molecular replacement | Model building | Structure refinement
Structure validation | Ligand fitting | Making geometry restraints | Structure deposition| All
Structure refinement | Structure validation | Making geometry restraints | Structure deposition| All
Phenix Documentation for Electron Microscopy (EM)
Map quality assessment | Structure refinement | Map statistics (resolution, etc) | Auto-sharpen a map | Calculate a local resolution map | Optimize a map with local anisotropic sharpening | Density modify a map | Dock a model into a map | Rapid model-building | Guess sequences from map | Flexibly fit a model to a map | Build a model | Making geometry restraints | Compare CA/P in two models | Identify symmetry in a map | Combine best parts of focused maps | Extract box with map and model | Convert map to structure factors | Segment a map | Adjust a CA/CB model | Fix register errors | All