Phenix help chatbot and AI analysis tool

You can use the Phenix chatbot to get help on using any Phenix program. Just ask it any question about using Phenix. You can also activate and use the Phenix AI analysis tool to summarize the results of a run in the GUI and suggest next steps.

• Instructions for using the chatbot
• Phenix AI analysis tool

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
• Calculate local resolution from two cryo-EM half-maps

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

• phenix.map_symmetry: Map symmetry analysis
• 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

• Predict AlphaFold2 models with phenix.predict_model
• 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

• Hints on writing scripts with AI tools
• Generating code documentation strings with with AI tools
• 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