Phenix: Difference between revisions

1,039 bytes added ,  15 August 2010
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''Preparation for molecular replacement:''
''Preparation for molecular replacement:''
* phenix.sculptor - automate selection and editing of molecular replacement (MR) models
* http://www.phenix-online.org/documentation/sculptor.htm phenix.sculptor - automate selection and editing of molecular replacement (MR) models
* phenix.ensembler - multiple superposition tool to automate construction of ensembles for MR
* http://www.phenix-online.org/documentation/ensembler.htm phenix.ensembler - multiple superposition tool to automate construction of ensembles for MR


''Preparation for refinement:''
''Preparation for refinement:''
* phenix.reel - restraints editor
* http://www.phenix-online.org/documentation/reel.htm phenix.reel - restraints editor especially for ligands


''Maps:''
''Maps:''
* phenix.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.real_space_correlation - compute correlation between two maps; can work with ensembles of structures
* phenix.real_space_correlation - compute correlation between two maps; can work with ensembles of structures. Seems to have no specific documentation.
* phenix.fobs_minus_fobs_map
* [http://www.phenix-online.org/documentation/get_cc_mtz_mtz.htm phenix.get_cc_mtz_mtz] - 
* phenix.multi_crystal_average
* phenix.fobs_minus_fobs_map - calculate difference density. Seems to have no specific documentation.
* phenix.grow_density - local density improvement, as originally described in Acta Cryst. (1997). D53, 540-543 (in development)
* [http://www.phenix-online.org/documentation/multi_crystal_average.htm phenix.multi_crystal_average] -
* 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 analysis and manipulation:
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''Model completion:''
''Model completion:''
* phenix.phase_and_build, phenix.build_one_model,
* 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
* phenix.fit_loops - fill short gaps using a loop library, and longer gaps (up to 15 residues) iteratively
* phenix.fit_loops - fill short gaps using a loop library, and longer gaps (up to 15 residues) iteratively
* phenix.assign_sequence
* [http://www.phenix-online.org/documentation/assign_sequence.htm phenix.assign_sequence] - Sequence assignment and linkage of neighboring segments with assign_sequence
* phenix.ligand_identification
* phenix.ligand_identification


''NCS usage:''
''NCS usage:''
* 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
* phenix.superpose_maps - transforms maps following a molecular superposition. Seems to have no specific documentation.
* phenix.apply_ncs
* [http://www.phenix-online.org/documentation/apply_ncs.htm phenix.apply_ncs] - applying NCS to a molecule to generate all NCS copiea


''Validation:''
''Validation:''
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