Overview of Phenix Programs
- 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
- 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
- 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
- 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
- phenix.process_predicted_model: Process AlphaFold2 and other predicted models
- phenix.dock_predicted_model: Dock processed AlphaFold2 models into cryo-EM map
- phenix.rebuild_predicted_model: Rebuild AlphaFold2 models into cryo-EM map based on docked domains
- phenix.dock_and_rebuild: Process, dock and rebuild AlphaFold2 model into cryo-EM map
- 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.build_rna_helices: Build RNA helices into a map
- phenix.combine_models: Take best parts of two models
- phenix.dock_and_rebuild: Process, dock and rebuild AlphaFold2 model into cryo-EM map
- phenix.dock_predicted_model: Dock processed AlphaFold2 models into cryo-EM map
- phenix.erraser: Run ERRASER
- phenix.find_helices_strands: Build helices and strands into a map
- phenix.fit_loops: Fit missing loops in a model
- phenix.map_to_model: Build a model using a low-resolution map or cryo-EM map
- phenix.rebuild_predicted_model: Rebuild AlphaFold2 models into cryo-EM map based on docked domains
- phenix.trace_and_build : Build a model by chain tracing using a cryo-EM map
- phenix.den_refine: Carry out DEN refinement of a model
- phenix.ensemble_refinement: run ensemble refinement
- phenix.find_tls_groups: Automatic identification of appropriate TLS groups in model
- phenix.ready_set: Set up files for refinement, including addition of hydrogens, generation of ligand restraints, and metal coordination restraints
- phenix.real_space_refine: Extensive real-space refinement
- phenix.refine: Carry out refinement of a model
- phenix.secondary_structure_restraints: generate pseudo H-bond restraints for alpha helices, beta sheets, and nucleic acid base pairs
- 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
- 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
- mmtbx.prepare_pdb_deposition: produce mmCIF files for deposition
- phenix.get_pdb_validation_report: get validation report from RCSB via OneDep API
- 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
Python-based
Hierarchical
ENvironment
for
Integrated
Xtallography