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Phenix: Difference between revisions
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A short help, such as usage and options, is printed out by all PHENIX command line tools: just type phenix.TOOLNAME and hit Enter (or Return). | A short help, such as usage and options, is printed out by all PHENIX command line tools: just type phenix.TOOLNAME and hit Enter (or Return). | ||
'''Main parts of the Phenix suite (possibly incomplete list!):''' | |||
* [http://www.phenix-online.org/documentation/refinement.htm phenix.refine] - refinement program | * [http://www.phenix-online.org/documentation/refinement.htm phenix.refine] - refinement program | ||
* [http://www.phenix-online.org/documentation/autosol.htm phenix.autosol] - "wizard" using HYSS, SOLVE, Phaser, RESOLVE, xtriage and phenix.refine to solve a structure and generate experimental phases with the MAD, MIR, SIR, or SAD methods | |||
* [http://www.phenix-online.org/documentation/automr.htm phenix.automr] - "wizard" providing an interface to Phaser molecular replacement and feeding the results of molecular replacement directly into the AutoBuild Wizard for automated model rebuilding | |||
* [http://www.phenix-online.org/documentation/autobuild.htm phenix.autobuild] - "wizard" for model rebuilding and completion. phenix.phase_and_build, phenix.build_one_model are fast ways to obtain results. | |||
* [http://www.phenix-online.org/documentation/ligandfit.htm phenix.ligandfit] - "wizard" carrying out fitting of flexible ligands to electron density maps | |||
* [http://www.phenix-online.org/documentation/elbow.htm phenix.elbow] - electronic Ligand Builder and Optimisation Workbench | |||
'''The following tools are also available (incomplete list):''' | |||
''Crystallographic data:'' | |||
* [http://www.phenix-online.org/documentation/xtriage.htm phenix.xtriage] - assessing data quality | * [http://www.phenix-online.org/documentation/xtriage.htm phenix.xtriage] - assessing data quality | ||
* [http://www.phenix-online.org/documentation/explore_metric_symmetry.htm phenix.explore_metric_symmetry] <font face="Courier">--unit_cell=145,44,67,90,110.5,90 --space_group=C2 --other_unit_cell=67,44,136,90,96,90 --other_space_group=p2</font> - investigate different settings | * [http://www.phenix-online.org/documentation/explore_metric_symmetry.htm phenix.explore_metric_symmetry] <font face="Courier">--unit_cell=145,44,67,90,110.5,90 --space_group=C2 --other_unit_cell=67,44,136,90,96,90 --other_space_group=p2</font> - investigate different settings | ||
* [http://www.phenix-online.org/documentation/reflection_statistics.htm phenix.reflection_statistics] - compare datasets (in 1 or 2 files) | * [http://www.phenix-online.org/documentation/reflection_statistics.htm phenix.reflection_statistics] - compare datasets (in 1 or 2 files) | ||
* [http://www.phenix-online.org/documentation/xmanip.htm phenix.xmanip] - Structure factor file manipulations | * [http://www.phenix-online.org/documentation/xmanip.htm phenix.xmanip] - Structure factor file manipulations | ||
* phenix.model_vs_data - not yet documented. Just use "phenix.model_vs_data model.pdb data.hkl" where data.hkl is a reflection file in most of known formats | * phenix.model_vs_data - not yet documented. Just use "phenix.model_vs_data model.pdb data.hkl" where data.hkl is a reflection file in most of known formats | ||
* [http://www.phenix-online.org/documentation/fmodel.htm phenix.fmodel] - calculate structure factors from model | * [http://www.phenix-online.org/documentation/fmodel.htm phenix.fmodel] - calculate structure factors from model | ||
* phenix.cif_as_mtz | |||
''Preparation for molecular replacement:'' | |||
* phenix.sculptor - automate selection and editing of molecular replacement (MR) models | |||
* phenix.ensembler - multiple superposition tool to automate construction of ensembles for MR | |||
''Preparation for refinement:'' | |||
* phenix.reel - restraints editor | |||
''Maps:'' | |||
* phenix.maps | |||
* phenix.real_space_correlation - compute correlation between two maps; can work with ensembles of structures | |||
* phenix.fobs_minus_fobs_map | |||
* phenix.multi_crystal_average | |||
* phenix.grow_density - local density improvement, as originally described in Acta Cryst. (1997). D53, 540-543 (in development) | |||
''Model analysis and manipulation: | |||
* [http://www.phenix-online.org/documentation/pdbtools.htm phenix.pbdtools] - PDB model manipulations and statistics; e.g. <font face="Courier">phenix.pbdtools your_model.pdb --show-adp-statistics</font> will show you complete statistics about B-factors; <font face="Courier">phenix.pbdtools your_model.pdb --show-geometry-statistics</font> will show you complete statistics about stereochemistry, <font face="Courier">phenix.pbdtools your_model.pdb set_b_iso=25.3 selection="chain A and resname ALA and name CA" </font>- this will set all B=25 for all CA atoms in all ALA residues of chain A. | |||
* [http://www.phenix-online.org/documentation/hydrogens.htm phenix.reduce] - tool for adding hydrogens to a PDB model | |||
* [http://www.phenix-online.org/documentation/superpose_pdbs.htm phenix.superpose_pdbs] - Superposition of models | |||
''Model completion:'' | |||
* phenix.phase_and_build, phenix.build_one_model, | |||
* [http://www.phenix-online.org/documentation/find_helices.htm phenix.find_helices] - rapid helix fitting to a map | |||
* phenix.fit_loops - fill short gaps using a loop library, and longer gaps (up to 15 residues) iteratively | |||
* phenix.assign_sequence | |||
* phenix.ligand_identification | |||
''NCS usage:'' | |||
* phenix.find_ncs - identification of NCS operators from protein coordinates (chains), heavy atom coordinates, or a density map | |||
* phenix.superpose_maps - transforms maps following a molecular superposition | |||
* phenix.apply_ncs | |||
''Validation:'' | |||
* [http://www.phenix-online.org/documentation/validation.htm#anch14 phenix.polygon] - starts the GUI and runs calculations resulting in a [http://dx.doi.org/10.1107/S0907444908044296 POLYGON] drawing of important characteristics of your PDB file in relation to the data | |||
* phenix.validate_model and phenix.validate are also GUI-only | |||
* phenix.ramalyze, phenix.rotalyze, and phenix.cbetadev | |||
* phenix.clashscore | |||
Below, the most important hints for the use of [http://www.phenix-online.org/documentation/refinement.htm phenix.refine] are given. | Below, the most important hints for the use of [http://www.phenix-online.org/documentation/refinement.htm phenix.refine] are given. | ||