Overview of Phenix Programs

Contents

General
Assessing data quality
Experimental Phasing
Molecular Replacement
Model Building
Structure Refinement
Validation
Ligands
Deposition
Reflection data tools
Map tools
Model tools
Miscellaneous

General

phenix: Run Phenix graphical user interface
phenix.about: Summarize contributors, packages, and info for phenix
phenix.acknowledgments: Summarize third-party components of Phenix
phenix.commands: List command line Phenix methods
phenix.doc: Phenix documentation
phenix.help: Load Phenix documentation (same as phenix.doc)
phenix.version: Print version of Phenix
phenix.find_program: Find a program or regression test
phenix.list: Print list of Phenix commands
phenix_regression.list: Print list of Phenix regression commands

Assessing data quality

phenix.cc_star: Calculate cc_star values for correlation of data vs resolution
phenix.compare_datasets: Similar to phenix.data_viewer, as side-by-side view
phenix.data_viewer: View pseudo-precession planes through a dataset
phenix.emma: Compare heavy-atom solutions
phenix.explore_metric_symmetry: Compare unit cells
phenix.merging_statistics: Calculate statistics on unmerged data
phenix.xtriage: Analyze data files for quality and unusual conditions

Experimental Phasing

phenix.autosol: Automated structure solution by MR/MAD/SAD
phenix.find_ncs: Find NCS in a model, map or heavy-atom sites
phenix.hyss: Identify heavy-atom sites from anomalous dataset
phenix.density_modification: Density modification
phenix.multi_crystal_average: Multi-crystal averaging
phenix.ncs_and_number_of_ha: Guess solvent content and number of heavy-atom sites
phenix.ncs_average: NCS average (no density modification) and write map file
phenix.phase_and_build: Rapid density modification and model-building

Molecular Replacement

phenix.adjust_robetta_resid: Apply sequence offset to a fragments file
phenix.automr: Automated MR and model-building
phenix.cut_out_density: Create MTZ coeffs with density cut out from a map
phenix.find_alt_orig_sym_mate: Superimpose structures allowing origin shifts (see also map_to_object)
phenix.morph_model: Morph a model to match a map
phenix.mr_model_preparation: Download and edit PDB files for MR
phenix.mr_rescoring: Model scoring for mr_rosetta
phenix.mr_rosetta: MR and model improvement with phaser/autobuild/Rosetta
phenix.mr_rosetta_rebuild: Rebuild model with Rosetta
phenix.phaser: Run PHASER
phenix.sculptor: Improve molecular replacment models using sequence alignment and structural infomation
phenix.ensembler: Superpose PDB files to create ensemble for MR
phenix.sculpt_ensemble: Combined sculptor and ensembler

Model Building

phenix.assign_sequence: Assign sequence to a chain using a map and seq file
phenix.autobuild: Iterative model-building density modification and refinement
phenix.build_one_model: Build one model using a map and data file
phenix.trace_and_build : Build a model by chain tracing using a cryo-EM map
phenix.map_to_model: Build a model using a low-resolution map or cryo-EM map
phenix.build_rna_helices: Build RNA helices into a map
phenix.combine_models: Take best parts of two models
phenix.erraser: Run ERRASER
phenix.find_helices_strands: Build helices and strands into a map
phenix.fit_loops: Fit missing loops in a model

Validation

phenix.b_factor_statistics: Display summary of atomic displacement parameters for a model (or atom selection)
phenix.cablam_training: C-alpha-based protein secondary structure exploration
phenix.cablam_validate: C-alpha-based protein secondary structure exploration
phenix.cbetadev: Validate protein sidechain C-beta geometry
phenix.clashscore: Evaluate model based on all-atom contacts
phenix.kinemage: Generates a multi-criterion validation kinemage file, for viewing in KiNG
phenix.king: Run KiNG molecular graphics
phenix.model_vs_data: Evaluate model using experimental data
phenix.model_vs_sequence: Detect residue mismatches in a PDB file
phenix.molprobity: Run molprobity
phenix.probe: Run PROBE, for analysis of all-atom contacts
phenix.r_factor_statistics: Distribution of Rfree, Rwork and Rfree-Rwork for PDB models at similar resolution
phenix.ramalyze: Validate protein backbone Ramachandran dihedral angles
phenix.reduce: Run REDUCE, software for addition or trimming of hydrogens
phenix.rna_validate: Validate RNA sugar puckers, backbone bond and angle geometry, and backbone suite conformations
phenix.rotalyze: Validate protein sidechain rotamers

Ligands

phenix.elbow: Ligand builder (CIF from PDB, SMILES etc)
phenix.find_all_ligands: Find ligands from a list in a map
phenix.ligand_identification: Identify ligands from a map
phenix.ligand_pipeline: Automated molecular replacement, refinement, and ligand fitting for high-throughput crystallography
phenix.ligandfit: Fit ligands into a map
phenix.metal_coordination: Generate metal coordination bond and angle restraints
phenix.reel: Graphical ligand restraints editor

Deposition

mmtbx.prepare_pdb_deposition: produce mmCIF files for deposition
phenix.get_pdb_validation_report: get validation report from RCSB via OneDep API

Reflection data tools

phenix.cif_as_mtz: Convert CIF to MTZ
phenix.cif_as_pdb: Convert CIF to PDB format
phenix.cns_as_mtz: Convert CNS to MTZ
phenix.csv_as_mtz: Convert csv reflection files to MTZ
phenix.fest: Experimental Delta F and FA estimation
phenix.fmodel: Calculate structure factors from model
phenix.import_and_add_free: Import a data file and add Free R set
phenix.mtz.dump: Dump MTZ file contents
phenix.mtz_as_cif: Convert mtz to CIF format
phenix.reciprocal_space_arrays: Create MTZ file with Fmodel,Fcalc,Fbulk,Fmask,FOM,HL, resolution and more
phenix.reflection_file_converter: Basic conversion between reflection file formats (command-line)
phenix.reflection_statistics: Evaluation and comparison of reflection data (e.g. anomalous difference correlations)
phenix.reindex: Reindex an MTZ file
phenix.remove_aniso: Remove anisotropy from columns of an MTZ dataset
phenix.xmanip: Experimental tool for manipulation of reflection data

Map tools

phenix.average_map_coeffs: Average a set of map coefficients from several files
phenix.composite_omit_map: Generate composite omit map, with our without refinement and simulated annealing
phenix.density_outside_model: Remove density near a model from a map
phenix.cut_out_density: Create MTZ coeffs with density cut out from a map
phenix.segment_and_split_map: Split a map into regions of density
phenix.auto_sharpen: Auto-sharpen/blur a map
phenix.local_aniso_sharpen: Optimize a map with local anisotropic sharpening
phenix.local_resolution: Calculate a local resolution map
phenix.dock_in_map: Dock a model into a map
phenix.map_symmetry: Identify symmetry in a map
phenix.resolve_cryo_em: Density modify a cryo-EM map
phenix.get_cc_mtz_mtz: Offset maps using allowed origin shifts and get correlation
phenix.guess_molecular_centers: Guess molecular centers from local RMS density
phenix.map_box: Simple cut out map around a PDB file
phenix.map_to_model_histogram: Compute averaged radial density distribution
phenix.map_to_object: Superimpose using SG symmetry only (see also find_alt_orig_sym_mate)
phenix.map_to_structure_factors: Calculate structure factors and HL coefficients from ccp4 map file and save in MTZ
phenix.map_value_at_point: Get map value at given coordinates
phenix.maps: Create maps from PDB and MTZ files
phenix.maximum_entropy_map: Compute maximum entropy map from map coefficients
phenix.polder: Compute omit map which excludes the bulk solvent around the omitted region
phenix.remove_free_from_map: Set all map coeffs of free reflections to zero
phenix.resolve_cryo_em: Density modify a cryo-EM map
phenix.superpose_maps: Superimpose PDB files and transform map to match
phenix.mtriage: Tool to analyse cryo-EM map (resolution, etc)

Model tools

phenix.apply_ncs: Apply NCS (.ncs_spec file) to a chain to create molecule
phenix.dynamics: Shake up structure with simple molecular dynamics
phenix.form_factor_query: f' and f'' table lookup given element and wavelength
phenix.get_cc_mtz_pdb: Offset PDB to match map using allowed origin shifts and get residue correlation
phenix.get_ligand_pdb: Create PDB file for a 3-letter ligand in the PDB
phenix.ksdssp: Identify secondary structure in a model
phenix.model_model_distances: Distance between two PDB files: per atom, residue, chain, model and overall
phenix.muscle: sequence alignment tool
phenix.pdb.hierarchy: Quick summary of PDB file content
phenix.pdb_as_cif: Convert PDB format to CIF
phenix.pdb_atom_selection: Extract selected atoms from PDB file (useful for experimenting with atom selections)
phenix.pdb_editor: Edit PDB files graphically
phenix.pdb_interpretation: Read PDB file and build restraints for refinement (useful for trouble-shooting)
phenix.pdbtools: Manipulate PDB files
phenix.perigee: Interaction finder
phenix.print_sequence: Print sequence from PDB file
phenix.pulchra: PULCHRA conversion from CA to full chain
phenix.simple_ncs_from_pdb: NCS from a PDB file (use instead phenix.find_ncs)
phenix.superpose_ligands: Superimpose two ligands
phenix.superpose_pdbs: Superimpose PDB files using aligned sequences
phenix.trim_pdb: Remove hydrogen atoms from a PDB file

Miscellaneous

phenix.default_gui_settings: Print out base PHENIX GUI configuration (mostly useful for site admins)
phenix.get_latest_version: Download most recent installer replacing current installation
phenix.grow_density: Density modification to enhance chain ends
phenix.pymol: Pymol
phenix.python: Run phenix-cognizant version of python
phenix.resolve: Run resolve
phenix.resolve_pattern: run resolve_pattern
phenix.run_example: Run an example from the phenix_examples directory
phenix.show_build_path: Show path to Phenix build directory
phenix.show_dist_paths: Show paths to all components of Phenix
phenix.solve: Run SOLVE
phenix.start_coot: Coot molecular graphics
phenix.where_mon_lib_list_cif: Show location of monomer library used by Phenix