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Phenix: Difference between revisions
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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.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 | * [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:'' | ||