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).


'''Main parts of the Phenix suite (possibly incomplete list!):'''
'''The following tools are available (list may be incomplete):'''
* [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''
 
''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


''Preparation for refinement:''
''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 analysis and manipulation:
''Model completion''
* [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 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
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