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Phenix: Difference between revisions
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The suite ([http://www.phenix-online.org/ Phenix home page]; [http://www.phenix-online.org/documentation documentation]) has a GUI program (phenix) which can be used to run the programs, but they also work from the command line. | The suite ([http://www.phenix-online.org/ Phenix home page]; [http://www.phenix-online.org/documentation documentation]) has a GUI program (phenix) which can be used to run the programs, but they also work from the command line. | ||
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). | ||
''' | '''The following tools are available (list may be incomplete):''' | ||
''Crystallographic data'' | |||
''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 | ||
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* phenix.cif_as_mtz | * phenix.cif_as_mtz | ||
''Preparation for molecular replacement | ''Experimental phasing'' | ||
* http://www.phenix-online.org/documentation/sculptor.htm phenix.sculptor - automate selection and editing of molecular replacement (MR) models | * [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/ensembler.htm phenix.ensembler - multiple superposition tool to automate construction of ensembles for MR | |||
''Preparation for molecular replacement'' | |||
* [http://www.phenix-online.org/documentation/sculptor.htm phenix.sculptor] - automate selection and editing of molecular replacement (MR) models | |||
* [http://www.phenix-online.org/documentation/ensembler.htm phenix.ensembler] - multiple superposition tool to automate construction of ensembles for MR | |||
''molecular replacement'' | |||
* [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 | |||
'' | ''Ligands'' | ||
* http://www.phenix-online.org/documentation/reel.htm phenix.reel - restraints editor especially for ligands | * http://www.phenix-online.org/documentation/reel.htm phenix.reel - restraints editor especially for ligands | ||
* [http://www.phenix-online.org/documentation/elbow.htm phenix.elbow] - electronic Ligand Builder and Optimisation Workbench | |||
''Model building and completion'' | |||
* [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 | |||
''Refinement'' | |||
* [http://www.phenix-online.org/documentation/refinement.htm phenix.refine] - refinement program; see more detailed usage description below. | |||
''Maps:'' | ''Maps:'' | ||
* phenix.maps - a command line tool to compute various maps. Seems to have no specific documentation. Can do B-factor sharpening for improving low-resolution maps. | * phenix.maps - a command line tool to compute various maps. Seems to have no specific documentation. Can do B-factor sharpening for improving low-resolution maps. | ||
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* phenix.grow_density - local density improvement, as originally described in Acta Cryst. (1997). D53, 540-543 (in development). Seems to have no specific documentation. | * phenix.grow_density - local density improvement, as originally described in Acta Cryst. (1997). D53, 540-543 (in development). Seems to have no specific documentation. | ||
''Model completion'' | |||
''Model completion | |||
* phenix.phase_and_build and phenix.build_one_model - fast autobuild | * phenix.phase_and_build and phenix.build_one_model - fast autobuild | ||
* [http://www.phenix-online.org/documentation/find_helices.htm phenix.find_helices] - rapid helix fitting to a map | * [http://www.phenix-online.org/documentation/find_helices.htm phenix.find_helices] - rapid helix fitting to a map | ||
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* phenix.ligand_identification | * phenix.ligand_identification | ||
''NCS usage | ''NCS usage'' | ||
* [http://www.phenix-online.org/documentation/find_ncs.htm phenix.find_ncs] - identification of NCS operators from protein coordinates (chains), heavy atom coordinates, or a density map | * [http://www.phenix-online.org/documentation/find_ncs.htm 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. Seems to have no specific documentation. | * phenix.superpose_maps - transforms maps following a molecular superposition. Seems to have no specific documentation. | ||
* [http://www.phenix-online.org/documentation/apply_ncs.htm phenix.apply_ncs] - applying NCS to a molecule to generate all NCS copiea | * [http://www.phenix-online.org/documentation/apply_ncs.htm phenix.apply_ncs] - applying NCS to a molecule to generate all NCS copiea | ||
''Validation | ''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 | |||
''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 | * [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.validate_model and phenix.validate are also GUI-only | ||