Phenix

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:

1. ) Rigid body refinement first cycle only (MZ protocol = VERY high convergence radius);
2. ) Refinement of individual xyz and b-factors every cycle with optimized weights;
3. ) Simulated annealing at 2nd and one before the last cycles;

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