P
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H
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vironment for
I
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Phenix Documentation - version unknown
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
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
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
Automated Model Building and Rebuilding using AutoBuild
(
GUI version
)
Low-resolution/cryo-EM model-building with map_to_model
Rapid model-building with find_helices_strands
Fitting loops with fit_loops
Rebuilding an RNA model with ERRASER
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
Frequently asked questions about model-building
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
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
Ligand fitting and restraints
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 map with cut_out_density
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
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
Idealize model geometry with phenix.geometry_minimization
Superimposing PDB files with phenix.superpose_pdbs
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
Shaking a structure with simple dynamcs
Sorting ligands and waters to group with polymer chains
Other tools 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