Phenix: Difference between revisions

362 bytes added ,  8 May 2009
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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:
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