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Phenix (edit)

Revision as of 14:02, 10 March 2014

14,444 bytes added ,  10 March 2014
new: List of programs
(new: List of programs)
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will split the total B-factor in ATOM records into TLS component and 'residual' part.
will split the total B-factor in ATOM records into TLS component and 'residual' part.
== List of programs ==
This is the output of phenix.list (version 1630):
<pre>
durandal.cluster_pdbs: Entropy-accelerated exact clustering of protein decoys
durandal.rank_pdbs: Entropy-accelerated exact clustering of protein decoys
fable.cout: Convert Fortran sources to C++
fable.show_calls: Show Fortran call graph
iotbx.cif.validate: Validation of CIF files against core CIF dictionary
iotbx.cns.transfer_crystal_symmetry: Read unit cell and space group from many file formats, add to CNS input file
iotbx.crystal_symmetry_from_any: Read unit cell and space group from many file formats
iotbx.dtrek.to_cns: Convert d*trek reflection file to CNS format
iotbx.lattice_symmetry: Determination of lattice symmetry given unit cell
iotbx.pdb.add_conformations: Add alternate conformation to a PDB file (for entire model or atom selection)
iotbx.pdb.join_fragment_files: Join multiple PDB files constituting one model
iotbx.pdb.link_as_geometry_restraints_edits: Convert PDB LINK records to phenix.refine parameter file format
iotbx.pdb.print_sequence: Extract FASTA sequence string from PDB file
iotbx.pdb_as_fasta: Extract FASTA sequence string from PDB file
iotbx.pdb_labels_comparison: Compare two pdb files, ignoring coordinates
iotbx.pdb_labels_diff: Diff between two pdb files, ignoring coordinates
iotbx.phil: Check syntax of parameter file
iotbx.r_free_flags_accumulation: Determine fraction of R-free flags as function of Miller indices sorted by resolution
iotbx.shelx.as_cif: Convert SHELX .ins or .res file to CIF format
iotbx.show_distances: Show interatomic distances given input in PDB format
labelit.image: Illustrate the raw data with marked up Bragg spots
labelit.pdf: Illustrate the raw data with marked up Bragg spots
mmtbx.lockit: Experimental command for real-space refinement, mainly ligands
mmtbx.mon_lib_cif_triage: Check syntax of monomer library CIF files
phaser.MRage: Molecular replacement pipeline
phaser.MRage.solutions: Calculates model and map from MRage results
phaser.domain_analysis: Determine domain boundaries from homologues
phaser.ensembler: Superpose PDB files to create ensemble for MR
phaser.sculptor: Improve molecular replacment models using sequence alignment and structural infomation
phaser.unit: Run phaser unittests
phenix: Run Phenix graphical user interface
phenix.about: Summarize contributors, packages, and info for phenix
phenix.acknowledgments: Summarize third-party components of Phenix
phenix.adjust_robetta_resid: Apply sequence offset to a fragments file
phenix.apply_ncs: Apply NCS (.ncs_spec file) to a chain to create molecule
phenix.assign_sequence: Assign sequence to a chain using a map and seq file
phenix.autobuild: Iterative model-building density modification and refinement
phenix.automr: Automated MR and model-building
phenix.autosol: Automated structure solution by MR/MAD/SAD
phenix.average_map_coeffs: Average a set of map coefficients from several files
phenix.b_factor_statistics: Display summary of atomic displacement parameters for a model (or atom selection)
phenix.build_one_model: Build one model using a map and data file
phenix.build_rna_helices: Build RNA helices into a map
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.cc_star: Calculate cc_star values for correlation of data vs resolution
phenix.cif_as_mtz: Convert CIF to MTZ
phenix.cif_as_pdb: Convert CIF to PDB format
phenix.clashscore: Evaluate model based on all-atom contacts
phenix.cns_as_mtz: Convert CNS to MTZ
phenix.combine_models: Take best parts of two models
phenix.commands: List command line Phenix methods
phenix.compare_datasets: Similar to phenix.data_viewer, as side-by-side view
phenix.composite_omit_map: Generate composite omit map, with our without refinement and simulated annealing
phenix.csv_as_mtz: Convert csv reflection files to MTZ
phenix.cut_out_density: Create MTZ coeffs with density cut out from a map
phenix.data_viewer: View pseudo-precession planes through a dataset
phenix.default_gui_settings: Print out base PHENIX GUI configuration (mostly useful for site admins)
phenix.den_refine: Carry out DEN refinement of a model
phenix.density_outside_model: Remove density near a model from a map
phenix.doc: Phenix documentation
phenix.dynamics: Shake up structure with simple molecular dynamics
phenix.elbow: Ligand builder (CIF from PDB, SMILES etc)
phenix.emma: Compare heavy-atom solutions
phenix.ensemble_refinement: run ensemble refinement
phenix.ensembler: Superpose PDB files to create ensemble for MR
phenix.erraser: Run ERRASER
phenix.explore_metric_symmetry: Compare unit cells
phenix.fest: Experimental Delta F and FA estimation
phenix.find_all_ligands: Find ligands from a list in a map
phenix.find_alt_orig_sym_mate: Superimpose structures allowing origin shifts (see also map_to_object)
phenix.find_helices_strands: Build helices and strands into a map
phenix.find_ncs: Find NCS in a model, map or heavy-atom sites
phenix.find_ncs_from_density: Find NCS from a map (use phenix.find_ncs)
phenix.find_tls_groups: Automatic identification of appropriate TLS groups in model
phenix.fit_loops: Fit missing loops in a model
phenix.fmodel: Calculate structure factors from model
phenix.form_factor_query: f' and f" table lookup given element and wavelength
phenix.get_cc_mtz_mtz: Offset maps using allowed origin shifts and get correlation
phenix.get_cc_mtz_pdb: Offset PDB to match map using allowed origin shifts and get residue correlation
phenix.get_latest_version: Download most recent installer replacing current installation
phenix.get_ligand_pdb: Create PDB file for a 3-letter ligand in the PDB
phenix.grow_density: Density modification to enhance chain ends
phenix.guess_molecular_centers: Guess molecular centers from local RMS density
phenix.help: Load Phenix documentation (same as phenix.doc)
phenix.hyss: Identify heavy-atom sites from anomalous dataset
phenix.import_and_add_free: Import a data file and add Free R set
phenix.kinemage: Generates a multi-criterion validation kinemage file, for viewing in KiNG
phenix.king: Run KiNG molecular graphics
phenix.ksdssp: Identify secondary structure in a model
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.list: Use instead: phenix.commands
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.merging_statistics: Calculate statistics on unmerged data
phenix.metal_coordination: Generate metal coordination bond and angle restraints
phenix.model_model_distances: Distance between two PDB files: per atom, residue, chain, model and overall
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.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.mtz.dump: Dump MTZ file contents
phenix.mtz2map: Convert MTZ file to map (superseded by phenix.maps)
phenix.mtz_as_cif: Convert mtz to CIF format
phenix.multi_crystal_average: Multi-crystal averaging
phenix.muscle: sequence alignment tool
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.old_gui: Run old version of Phenix GUI
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.phase_and_build: Rapid density modification and model-building
phenix.phaser: Run PHASER
phenix.print_sequence: Print sequence from PDB file
phenix.probe: Run PROBE, for analysis of all-atom contacts
phenix.pulchra: PULCHRA conversion from CA to full chain
phenix.pymol: Pymol
phenix.python: Run phenix-cognizant version of python
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.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.reciprocal_space_arrays: Create MTZ file with Fmodel,Fcalc,Fbulk,Fmask,FOM,HL, resolution and more
phenix.reduce: Run REDUCE, software for addition or trimming of hydrogens
phenix.reel: Graphical ligand restraints editor
phenix.refine: Carry out refinement of a model
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.remove_free_from_map: Set all map coeffs of free reflections to zero
phenix.resolve: Run resolve
phenix.resolve_pattern: run resolve_pattern
phenix.rna_validate: Validate RNA sugar puckers, backbone bond and angle geometry, and backbone suite conformations
phenix.rotalyze: Validate protein sidechain rotamers
phenix.run_example: Run an example from the phenix_examples directory
phenix.sculptor: Improve molecular replacment models using sequence alignment and structural infomation
phenix.secondary_structure_restraints: generate pseudo H-bond restraints for alpha helices, beta sheets, and nucleic acid base pairs
phenix.show_build_path: Show path to Phenix build directory
phenix.show_dist_paths: Show paths to all components of Phenix
phenix.simple_ncs_from_pdb: NCS from a PDB file (use instead phenix.find_ncs)
phenix.solve: Run SOLVE
phenix.start_coot: Coot molecular graphics
phenix.superpose_ligands: Superimpose two ligands
phenix.superpose_maps: Superimpose PDB files and transform map to match
phenix.superpose_pdbs: Superimpose PDB files using aligned sequences
phenix.trim_pdb: Remove hydrogen atoms from a PDB file
phenix.version: Print version of Phenix
phenix.where_mon_lib_list_cif: Show location of monomer library used by Phenix
phenix.xmanip: Experimental tool for manipulation of reflection data
phenix.xtriage: Analyze data files for quality and unusual conditions
phenix_regression.phenix_doc.test_phenix_html: Test generation of documentation
phenix_regression.run_tests_mp: Run solve-resolve tests in parallel
phenix_regression.test_all_parallel: Test wizards
phenix_regression.test_apps: Relatively short tests of selected major phenix applications
phenix_regression.test_rosetta_refine: Test rosetta refine
phenix_regression.testwizard: Run wizard tests
phenix_regression.wizards.list: list all wizard regression tests
phenix_regression.wizards.test_all: Run all wizard tests
phenix_regression.wizards.test_all_parallel: Run all wizard tests in parallel
phenix_regression.wizards.test_command_line: General wizard tests
phenix_regression.wizards.test_command_line_build: Wizard model-building tests
phenix_regression.wizards.test_command_line_ligands: Wizard ligand-building tests
phenix_regression.wizards.test_command_line_loops: Wizard loop-fitting tests
phenix_regression.wizards.test_command_line_misc: misc wizard tests
phenix_regression.wizards.test_command_line_ncs: Wizard NCS tests
phenix_regression.wizards.test_command_line_non_standard: Wizard non-standard SG tests
phenix_regression.wizards.test_command_line_omit: Wizard omit tests
phenix_regression.wizards.test_command_line_resolve_memory: resolve in memory
phenix_regression.wizards.test_command_line_rosetta: mr_rosetta tests
phenix_regression.wizards.test_command_line_rosetta_iter: multi-cycle mr_rosetta tests
phenix_regression.wizards.test_command_line_rosetta_quick: quick mr_rosetta tests
phenix_regression.wizards.test_command_line_trace: tests of trace_chain
phenix_regression.wizards.test_commands_in_doc: Test Wizard commands in documentation
phenix_regression.wizards.test_help: Test Wizard help commands
phenix_regression.wizards.test_input_files: Test data files in Wizards
phenix_regression.wizards.test_labels: Test various label formats in Wizards
phenix_regression.wizards.test_map_to_object: Test map_to_object
phenix_regression.wizards.test_maps_only: Test making maps in wizards
phenix_regression.wizards.test_misc_methods: Test misc Wizard methods
phenix_regression.wizards.test_missing_data: Test Wizards with missing data
phenix_regression.wizards.test_mult: Test multiple-model autobuild
phenix_regression.wizards.test_multi: Test multi-crystal averaging
phenix_regression.wizards.test_ncs: Test NCS identification
phenix_regression.wizards.test_ncs_in_phenix_refine: Test using NCS in phenix.refine
phenix_regression.wizards.test_omit: Test omit maps
phenix_regression.wizards.test_omit_lig: Test omit maps with ligand
phenix_regression.wizards.test_residue_codes: Test residue names
phenix_regression.wizards.test_resno: Test rebuild_in_place residue numbers
phenix_regression.wizards.test_resolve: Run comprehensive solve/resolve tests
phenix_regression.wizards.test_short_seq: Test Wizards with short sequence
</pre>


== Tips and Tricks ==
== Tips and Tricks ==
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