Python-based Hierarchical ENvironment for Integrated Xtallography

PHENIX Documentation - version 1.6.4-486

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 main modules in PHENIX
   6. FAQS: Frequently asked questions
   7. Index for PHENIX documentation
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 manipulating 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; generate metal coordination files; introduce neutron exchange sites using ReadySet!
   7. Generating hydrogen atoms for refinement using phenix.reduce
6. The PHENIX graphical user interface
   1. Overview and main GUI
   2. Graphical editor for MTZ files
   3. The Xtriage GUI
   4. Molecular replacement in the Phaser GUI
   5. SAD phasing in the Phaser GUI
   6. The phenix.refine graphical interface
   7. Validation tools in PHENIX
   8. Generating electron density maps
7. 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 model-building with find_helices_strands
   7. Fitting loops with fit_loops
   8. Rapid iterative map improvement and model-building with phase_and_build
   9. Find NCS in a map with find_ncs_from_density
   10. Generating NCS copies with apply_ncs
   11. Rapid model-building with build_one_model
   12. Assigning sequence to a model with assign_sequence
   13. Replace side chains with rotamers using replace_side_chains
   14. Remove test set reflections from a map using remove_free_from_map
   15. Guessing molecular centers in a map with guess_molecular_centers
   16. PDB model: statistics, manipulations and more with phenix.pdbtools
   17. Ensembler: create ensemble of models for molecular replacement
   18. Sculptor: modify input model for molecular replacement
   19. phenix.fmodel: structure factors from a PDB file
   20. Running SOLVE/RESOLVE in PHENIX
   21. Automated ligand identification in PHENIX
   22. Finding all the ligands in a map with phenix.find_all_ligands
   23. Map one PDB file close to another using SG symmetry with phenix.map_to_object
   24. PyMOL in PHENIX
8. Useful tools outside of PHENIX
   1. Manual model inspection and building with Coot
   2. MolProbity - An Active Validation Tool
9. 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
10. Appendix
    1. PHENIX html documentation generation procedures