P
ython-based
H
ierarchical
EN
vironment for
I
ntegrated
X
tallography
Phenix Documentation - version 1.21.2-5419
Introduction to Phenix
What is Phenix
How to install and run Phenix
The Phenix graphical interface
The main modules in Phenix
Phenix atom selection syntax
FAQS: Frequently asked questions
Dictionary of common terms
Overview of file formats
Index for Phenix documentation
Tutorials and Examples
Finding a program or regression test in Phenix
Tools for analysing and manipulating experimental data in Phenix
Data quality assessment with phenix.xtriage
(
GUI version
)
Planning a SAD experiment with phenix.plan_sad_experiment
Scaling unmerged anomalous data or multiple datasets with phenix.scale_and_merge
Analyzing anomalous signal in a SAD experiment with phenix.anomalous_signal
Data quality assessment with phenix.reflection_statistics
Structure factor file inspection and conversions
Graphical editor for MTZ files
Manipulating reflection data with phenix.xmanip
Exploring the symmetry of your crystal with phenix.explore_metric_symmetry
Importing data from the PDB with phenix.cif_as_mtz
Visualizing reciprocal-space data
Using unmerged data in Phenix
Showing information about a map file
Experimental phasing
Automated Structure Solution using AutoSol
(
GUI version
)
SAD phasing in the Phaser GUI
Substructure determination with phenix.hyss
Comparison of substructure sites with phenix.emma
Setting up SAD data from the PDB with phenix.sad_data_from_pdb
Frequently asked questions about experimental phasing
Molecular replacement
Overview of molecular replacement in Phenix
Molecular replacement in the Phaser GUI
MRage: automated molecular replacement
MR and model building with AutoMR, AutoBuild and Rosetta
Morphing a poor model into electron density
Documentation for the Phaser program
Ensembler: create ensemble of models for molecular replacement
Sculptor: modify input model for molecular replacement
Frequently asked questions about molecular replacement
Model-building
Solve an X-ray structure or interpret a cryo-EM map with PredictAndBuild
Automated Model Building and Rebuilding using AutoBuild
(
GUI version
)
Rapid cryo-EM model-building with trace_and_build
Dock chains in Cryo-EM map with dock_in_map
Likelihood-based single model docking in Cryo-EM map with em_placement
Dock AlphaFold model with dock_predicted_model
Dock and rebuild AlphaFold model with dock_and_rebuild
Cryo-EM model rebuilding with rebuild_model
Cryo-EM model completion with model_completion
Cryo-EM model-building with Pathwalker
Low-resolution/cryo-EM model-building with map_to_model
Rapid model-building with find_helices_strands
Fitting loops with fit_loops
Building starting with a very poor map with parallel_autobuild
Rapid iterative map improvement and model-building with phase_and_build
Rapid model-building with build_one_model
Assigning sequence to a model with assign_sequence
Replace side chains with rotamers using replace_side_chains
Combine the best parts of two models with combine_models
Remove incorrect protein from complex with remove_poor_fragments
Fixing register errors with fix_insertions_deletions
Adjusting a CA/CB model with refine_ca_model
Frequently asked questions about model-building
Build water into cryo-EM map
Structure refinement and restraint generation
Structure refinement with phenix.refine
(
GUI version
)
Determining non-crystallographic symmetry (NCS) from a PDB file with phenix.simple_ncs_from_pdb
Finding and analyzing NCS from heavy-atom sites or a model with phenix.find_ncs
Generating ligand coordinates and restraints using eLBOW
(
GUI version
)
Editing ligand restraints from eLBOW using REEL
Add hydrogens; generate metal coordination files; introduce neutron exchange sites using ReadySet!
Adding secondary structure restraints
Mode idealization before refinement
Generating hydrogen atoms for refinement using phenix.reduce
Refinement in real space with phenix.real_space_refine
Ensemble refinement
Variability refinement
DEN refinement with phenix.den_refine
Hybrid Rosetta/Phenix refinement of protein X-ray crystal structures
Hybrid Phenix/Amber refinement for protein and RNA/DNA X-ray crystal structure
Hybrid Phenix/AFITT refinement for ligands in X-ray crystal structure
Frequently asked questions (FAQs) about phenix.refine
Validation
Validation in the Phenix GUI
phenix.model_vs_data: compute model, data and model-to-data fit statistics
Low-resolution secondary structure validation with CaBLAM
Map statistics (resolution, etc) with Mtriage
phenix.get_pdb_validation_report: get validation report from RCSB via OneDep API
Ligand fitting and restraints
Quantum Interface (QI)
Automated Ligand Fitting using LigandFit
(
GUI version
)
Automated Ligand Fitting using Guided Ligand Replacement (GLR)
Automated ligand identification in Phenix
Finding all the ligands in a map with phenix.find_all_ligands
Generating ligand coordinates and restraints using eLBOW
(
GUI version
)
Editing ligand restraints from eLBOW using REEL
Automated protein-ligand structure determination with phenix.ligand_pipeline
Frequently asked questions about ligand fitting and restraints
Carbohydrates
Carbohydrate Primer
Adding Carbohydrates using CarboLoad
Simple Carbohydrate Line-Entry System (SCaLES)
Building Carbohydrates with a GUI
Map utilities
Generating electron density maps in the GUI
phenix.maps: tool to compute various maps and save them in most of known formats
Generating composite omit maps
phenix.map_value_at_point: compute map value at a given point
phenix.mtz2map: FFT-ing map coefficients
phenix.ncs_average: Simple NCS averaging
phenix.polder: compute omit map excluding bulk solvent
Correlation of map and model with get_cc_mtz_pdb
Correlation of two maps with origin shifts with get_cc_mtz_mtz
Cut out density from a crystallographic map with cut_out_density
Cut out density from a cryo-EM or crystallographic map with map_box
Segment a cryo-EM map with segment_and_split_map
Compare CA positions in two models with chain_comparison
Auto-sharpen/blur a cryo-EM map with auto_sharpen
Apply anisotropic sharpening to a cryo-EM map with local_aniso_sharpen
Combine cryo-EM maps with combine_focused_maps
Density modify a cryo-EM map with resolve_cryo_em
Remove test set reflections from a map using remove_free_from_map
Guessing molecular centers in a map with guess_molecular_centers
Density modification with phenix.density_modification
Density modification with multi-crystal averaging with phenix.multi_crystal_average
Find NCS in a map with find_ncs_from_density
Map superposition with phenix.superpose_maps
Modify map coefficients to remove density near a model
phenix.fem: compute Feature Enhanced Map (FEM)
Residual difference map analysis with phenix.find_peaks_holes
Convert map into structure factors phenix.map_to_structure_factors
Model utilities
Process AlphaFold2 and other predicted models with phenix.process_predicted_model
Idealize model geometry with phenix.geometry_minimization
LSQ-Superimpose models with phenix.superpose_pdbs
SSM-Superimpose and morph models
Generating NCS copies with apply_ncs
PDB model: statistics, manipulations and more with phenix.pdbtools
phenix.fmodel: structure factors from a PDB file
phenix.f000: given PDB file and mean bulk-solvent density estimate F(0,0,0)
Map one PDB file close to another using SG symmetry with phenix.map_to_object
SCEDS - identify domains with normal mode analysis
structural_domains_search - identify domains using a graph search
Find symmetry equivalent molecular replacement solution on alternative origin with phenix.find_alt_orig_sym_mate
Building biological assembly and crystallographic asymmetric unit
Calculating Fragment Antigen-Binding (Fab) elbow angle
Find Similar Structures in PDB using phi-psi angles and sequence
Find Structures in PDB using SSM matching and morphing
Find fragments in PDB matching a target fragment
Replace model with fragments from the PDB
Shaking a structure with simple dynamcs
Sorting ligands and waters to group with polymer chains
Trim one model to avoid atoms in another with trim_overlapping
Other tools in Phenix
Finding a program or regression test in Phenix
Characterizing raw data and model with LABELIT
Running SOLVE/RESOLVE in Phenix
Parallel validation and analysis of related structures
phenix.reciprocal_space_arrays: compute various arrays such as Fcalc, Fmask, Fbulk, HL ...
Generating Table 1 for publication
Useful tools outside of Phenix
Manual model inspection and building with Coot
Molecular graphics with PyMOL
MolProbity - An **Active** Validation Tool
Appendix
Phenix html documentation generation procedures
Phenix Windows build procedures
Bundling base components as zip files for the Windows build
Creating a Windows installer for PHENIX
Python-based
Hierarchical
ENvironment
for
Integrated
Xtallography