Phenix: Difference between revisions

91 bytes added ,  27 August 2010
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== Experimental phasing ==
== Experimental phasing ==
* [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/autosol.htm phenix.autosol] - experimental phasing "wizard" ===
 
phenix.autosol uses HYSS, SOLVE, Phaser, RESOLVE, xtriage and phenix.refine to solve a structure and generate experimental phases with the MAD, MIR, SIR, or SAD methods  


== Molecular replacement ==
== 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 molecular replacement ===
=== [http://www.phenix-online.org/documentation/automr.htm phenix.automr] - interface to Phaser and Resolve ===
* [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
This "wizard" provides an interface to Phaser molecular replacement and feeds the results of molecular replacement directly into the AutoBuild Wizard for automated model rebuilding
 
=== [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 ===


== Ligands ==
== 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
=== [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 ==
== 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/autobuild.htm phenix.autobuild] - "wizard" for model rebuilding and completion ===
* [http://www.phenix-online.org/documentation/ligandfit.htm phenix.ligandfit] - "wizard" carrying out fitting of flexible ligands to electron density maps
 
* phenix.phase_and_build and  phenix.build_one_model - fast autobuild
phenix.phase_and_build, phenix.build_one_model are fast ways to obtain results.
* [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
=== [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/assign_sequence.htm phenix.assign_sequence] - Sequence assignment and linkage of neighboring segments with assign_sequence
=== phenix.phase_and_build and  phenix.build_one_model - fast autobuild ===
* phenix.ligand_identification
=== [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 ===
=== [http://www.phenix-online.org/documentation/assign_sequence.htm phenix.assign_sequence] - sequence assignment and linkage of neighboring segments ===
=== phenix.ligand_identification ===


== Refinement with [http://www.phenix-online.org/documentation/refinement.htm phenix.refine] ==
== Refinement with [http://www.phenix-online.org/documentation/refinement.htm phenix.refine] ==
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