Phenix Documentation - version unknown

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

Working with AlphaFold2, RoseTTAFold and other predicted models

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

Crystallographic Structure Solution with Phenix

Data Quality Experimental phasing Molecular replacement Density Modification Model building Structure refinement Structure validation Ligands Structure Deposition
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

Phenix Documentation for Neutron Crystallography

Structure refinement | Structure validation | Making geometry restraints | Structure deposition| All

Cryo-EM Structure Solution with Phenix

Auto-sharpen map Dock a model into a cryo-EM map Autobuild a model into a cryo-EM map Optimize an atomic model with respect to the map and prior chemical knowledge Validate data and a structure with respect to prior chemical knowledge Deposit model and data at the world wide Protein Data Bank
Phenix Documentation for Electron Microscopy (EM)
Map quality assessment | Map symmetry | 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 | Build ordered water | All