Python-based Hierarchical ENvironment for Integrated Xtallography

PHENIX Documentation - version 1.8-1069

  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 interface
    6. The main modules in PHENIX
    7. FAQS: Frequently asked questions
    8. Glossary of common terms
    9. Index for PHENIX documentation
  2. The PHENIX Wizards for Automation
    1. Using the PHENIX Wizards
    2. Automated Structure Solution using AutoSol (GUI version)
    3. Automated Molecular Replacement using AutoMR (GUI version)
    4. Automated Model Building and Rebuilding using AutoBuild (GUI version)
    5. Automated Ligand Fitting using LigandFit (GUI version)
  3. Tools for analysing and manipulating experimental data in PHENIX
    1. Data quality assessment with phenix.xtriage (GUI version)
    2. Data quality assessment with phenix.reflection_statistics
    3. Structure factor file inspection and conversions
    4. Graphical editor for MTZ files
    5. Manipulating reflection data with phenix.xmanip
    6. Exploring the symmetry of your crystal with phenix.explore_metric_symmetry
    7. Importing data from the PDB with phenix.cif_as_mtz
    8. Visualizing reciprocal-space data
  4. Experimental phasing
    1. Automated Structure Solution using AutoSol (GUI version)
    2. SAD phasing in the Phaser GUI
    3. Substructure determination with phenix.hyss
    4. Comparison of substructure sites with phenix.emma
  5. Molecular replacement
    1. Overview of molecular replacement in PHENIX
    2. Automated Molecular Replacement using AutoMR
    3. Molecular replacement in the Phaser GUI
    4. MR and model building with AutoMR, AutoBuild and Rosetta
    5. Morphing a poor model into electron density
    6. Documentation for the Phaser program
    7. Ensembler: create ensemble of models for molecular replacement
    8. Sculptor: modify input model for molecular replacement
  6. Model-building
    1. Automated Model Building and Rebuilding using AutoBuild (GUI version)
    2. Rapid model-building with find_helices_strands
    3. Fitting loops with fit_loops
    4. Rapid iterative map improvement and model-building with phase_and_build
    5. Rapid model-building with build_one_model
    6. Assigning sequence to a model with assign_sequence
    7. Replace side chains with rotamers using replace_side_chains
    8. Combine the best parts of two models
  7. Structure refinement and restraint generation
    1. Structure refinement with phenix.refine (GUI version)
    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 (GUI version)
    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
    8. DEN refinement with phenix.den_refine
    9. Frequently asked questions (FAQs) about phenix.refine
  8. Validation
    1. Validation in the PHENIX GUI
    2. phenix.model_vs_data: compute model, data and model-to-data fit statistics
  9. Ligand fitting and restraints
    1. Automated Ligand Fitting using LigandFit (GUI version)
    2. Automated ligand identification in PHENIX
    3. Finding all the ligands in a map with phenix.find_all_ligands
    4. Generating ligand coordinates and restraints using eLBOW (GUI version)
    5. Editing ligand restraints from eLBOW using REEL
  10. Map utilities
    1. Generating electron density maps in the GUI
    2. phenix.maps: tool to compute various maps and save them in most of known formats
    3. phenix.map_value_at_point: compute map value at a given point
    4. phenix.mtz2map: FFT-ing map coefficients
    5. phenix.ncs_average: Simple NCS averaging
    6. Correlation of map and model with get_cc_mtz_pdb
    7. Correlation of two maps with origin shifts with get_cc_mtz_mtz
    8. Cut out density from a map with cut_out_density
    9. Remove test set reflections from a map using remove_free_from_map
    10. Guessing molecular centers in a map with guess_molecular_centers
    11. Density modification with multi-crystal averaging with phenix.multi_crystal_average
    12. Find NCS in a map with find_ncs_from_density
    13. Map superposition with phenix.superpose_maps
  11. Model utilities
    1. Superimposing PDB files with phenix.superpose_pdbs
    2. Generating NCS copies with apply_ncs
    3. PDB model: statistics, manipulations and more with phenix.pdbtools
    4. phenix.fmodel: structure factors from a PDB file
    5. Map one PDB file close to another using SG symmetry with phenix.map_to_object
  12. Other tools in PHENIX
    1. Running SOLVE/RESOLVE in PHENIX
    2. Parallel validation and analysis of related structures
    3. phenix.reciprocal_space_arrays: compute various arrays such as Fcalc, Fmask, Fbulk, HL ...
  13. Characterizing raw data and model with LABELIT
    1. Documentation to be added in the next build
    2. For now, please refer to the LABELIT Web page
  14. Useful tools outside of PHENIX
    1. Manual model inspection and building with Coot
    2. Molecular graphics with PyMOL
    3. MolProbity - An Active Validation Tool
  15. 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
    13. Running refinement examples on the command line
  16. Appendix
    1. PHENIX html documentation generation procedures