Phenix help chatbot

You can use the Phenix chatbot to get help on using any Phenix program. Just ask it any question about using Phenix.

• Instructions for using the chatbot

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-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
• Create a model with alternative side-chain conformations with phenix.create_alt_conf
• Analyze a model with alternative side-chain conformations with phenix.analyze_alt_conf

Structure refinement and restraint generation

• AQuaRef: AI-enabled Quantum Refinement of macromolecular models <AQuaRef.html>
• 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
• Model geometry evaluation with phenix.holton_geometry_validation

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
• Simple Carbohydrate Line-Entry System (SCaLES)

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 maps or map and model with map_correlations
• 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
• Optimize an Xray or cryo-EM map with map_sharpening
• 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
• Superimpose models with phenix.superpose_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

• Setting up GUI tests in Phenix
• Finding a program or regression test in Phenix
• Running regression tests 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