Python-based Hierarchical ENvironment for Integrated Xtallography

PHENIX Documentation - version 1.4

1. Introduction to PHENIX
   1. What is PHENIX
   2. How to install PHENIX
   3. How to set up your environment to use PHENIX
   4. Running PHENIX
   5. The PHENIX Graphical User Interface
   6. The main modules in PHENIX
   7. FAQS: Frequently asked questions
2. The PHENIX Wizards for Automation
   1. Using the PHENIX Wizards
   2. Automated Structure Solution using AutoSol
   3. Automated Molecular Replacement using AutoMR
   4. Automated Model Building and Rebuilding using AutoBuild
   5. Automated Ligand Fitting using LigandFit
3. Tools for analysing and manupulating experimental data in PHENIX
   1. Data quality assessment with phenix.xtriage
   2. Data quality assessment with phenix.reflection_statistics
   3. Structure factor file inspection and conversions
   4. Manipulating reflection data with phenix.xmanip
   5. Exploring the symmetry of your crystal with phenix.explore_metric_symmetry
4. Tools for substructure Determination in PHENIX
   1. Substructure determination with phenix.hyss
   2. Comparison of substructure sites with phenix.emma
5. Tools for structure refinement and restraint generation in PHENIX
   1. Structure refinement with phenix.refine
   2. Determining non-crystallographic symmetry (NCS) from a PDB file with phenix.simple_ncs_from_pdb
   3. Finding and analyzing NCS from heavy-atom sites or a model with phenix.find_ncs
   4. Generating ligand coordinates and restraints using eLBOW
   5. Editing ligand restraints from eLBOW using REEL
   6. Add hydrogens to protein, ligands and water molecules; generate metal coordination files; and introduce neutron exchange sites using ReadySet! (phenix.ready_set)
   7. Generating hydrogen atoms for refinement using phenix.reduce
6. Other tools in PHENIX
   1. Documentation for the Phaser program
   2. Superimposing PDB files with phenix.superpose_pdbs
   3. Density modification with multi-crystal averaging with phenix.multi_crystal_average
   4. Correlation of map and model with get_cc_mtz_pdb
   5. Correlation of two maps with origin shifts with get_cc_mtz_mtz
   6. Rapid secondary structure fitting to a map with find_helices_strands
   7. PDB model: statistics, manipulations, Fcalc and more with phenix.pdbtools
   8. Running SOLVE/RESOLVE in PHENIX
   9. Automated ligand identification in PHENIX
   10. Finding all the ligands in a map with phenix.find_all_ligands
   11. Map one PDB file close to another using SG symmetry with phenix.map_to_object
   12. PyMOL in PHENIX
7. Useful tools outside of PHENIX
   1. Manual model inspection and building with Coot
   2. MolProbity - An Active Validation Tool
8. PHENIX Examples and Tutorials
   1. PHENIX examples
   2. Tutorial 1: Solving a structure using SAD data
   3. Tutorial 2: Solving a structure using MAD data
   4. Tutorial 3: Solving a structure using MIR data
   5. Tutorial 4: Iterative model-building, density modification and refinement starting from experimental phases
   6. Tutorial 5: Solving a structure using Molecular Replacement
   7. Tutorial 6: Automatically rebuilding a structure solved by Molecular Replacement
   8. Tutorial 7: Fitting a flexible ligand into a difference electron density map
   9. Tutorial 8: Structure refinement
   10. Tutorial 9: Refining a structure in the presence of merohedral twinning
   11. Tutorial 10: Generating ligand coordinates and restraints for structure refinement
   12. Tutorial 11: Structure validation using MolProbity
9. Appendix
   1. PHENIX html documentation generation procedures
10. Index