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PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is a new software suite for the automated determination and refinement of macromolecular structures using X-ray crystallography and other methods. It integrates well with CCP4-formatted files for I/O, is highly automated, and very straightforward to use. | PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is a new software suite for the automated determination and refinement of macromolecular structures using X-ray crystallography and other methods. It integrates well with CCP4-formatted files for I/O, is highly automated, and very straightforward to use. | ||
== Example == | |||
% phenix.refine model.pdb data.mtz strategy=rigid_body+individual_sites+individual_adp \ | |||
simulated_annealing=true optimize_wxc=true optimize_wxu=true main.number_of_macro_cycles=5 | |||
Here "data.mtz" is your reflection data file. PHENIX automatically recognizes most of the known file formats, so it can be MTZ, CNS or ... | |||
This will do the following: | |||
#) Rigid body refinement first cycle only (MZ protocol = VERY high convergence radius); | |||
#) Refinement of individual xyz and b-factors every cycle with optimized weights; | |||
#) Simulated annealing at 2nd and one before the last cycles; | |||
[http://www.phenix-online.org/ Phenix home page] | [http://www.phenix-online.org/ Phenix home page] | ||