Phenix Documentation - 1.16-3549

Phenix programs and their functions
The Phenix graphical interface
Overview of video tutorials
Tutorials and Examples
Dictionary of crystallographic and other terms
FAQs: Frequently asked questions
How to install, setup and run Phenix
Complete Phenix reference documentation
Bibliography
Index

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)
Structure refinement | Map statistics (resolution, etc) | Auto-sharpen 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