Phenix developers doc

Introduction: Introduction high level model building tools.
Reading files: Learn how to set up example files.
Fitting ligands: How to fit a ligand into density inside a box.
Model building: How to build a model into density and extend a chain.
Loop fitting: How to build and fit a loop.
Replace a segment: How to replace part of a model and how to create a composite model.
Morphing: How to adjust a model by morphing it to match the density in a map.
Sequence Assignment: How to assign a sequence to a model or to guess the sequence from the density.

Restraint jiffys: Useful ways to display .geo files and see particular restraints.
Programming: Specific tips for programming in Phenix
- Creating a program with the Program Template: Step by step instructions on how to use the program template.
- Runsnake: How to do profiling with Runsnake.

Table of contents