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Phenix: Difference between revisions
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== Example for use of phenix.refine == | == Example for use of phenix.refine == | ||
=== basic usage === | |||
phenix.refine model.pdb data.mtz | |||
=== advanced usage === | |||
phenix.refine model.pdb data.mtz strategy=rigid_body+individual_sites+individual_adp \ | 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 | simulated_annealing=true optimize_wxc=true optimize_wxu=true main.number_of_macro_cycles=5 | ||
Warning: optimize_wxc=true optimize_wxu=true makes the program use '''much''' more time! | |||
Here "data.mtz" is your reflection data file. PHENIX automatically recognizes most of the known file formats, so it can be MTZ, CNS or ... | Here "data.mtz" is your reflection data file. PHENIX automatically recognizes most of the known file formats, so it can be MTZ, CNS or ... | ||
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# Simulated annealing at 2nd and one before the last cycles; | # Simulated annealing at 2nd and one before the last cycles; | ||
''Warning'': the file model.pdb in this example should '''not''' have any '''ANISOU''' records! If it has any, these would be refined as individual anisotropic which is most likely not desired. | |||
== Ligands == | == Ligands == | ||
If some ligand in model.pdb is unknown, phenix.refine will complain: | If some ligand in model.pdb is unknown, phenix.refine will complain: | ||