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Phenix: Difference between revisions
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→advanced usage: new nomenclature: optimize_xyz_weight=true optimize_adp_weight=true
(→advanced usage: new nomenclature: optimize_xyz_weight=true optimize_adp_weight=true) |
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==== advanced usage ==== | ==== 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 | simulated_annealing=true optimize_xyz_weight=true optimize_adp_weight=true main.number_of_macro_cycles=5 \ | ||
ordered_solvent=True | ordered_solvent=True | ||
| Line 216: | Line 216: | ||
# Rigid body refinement first cycle only (MZ protocol = VERY high convergence radius); | # Rigid body refinement first cycle only (MZ protocol = VERY high convergence radius); | ||
# Refinement of individual xyz and b-factors every cycle with optimized weights ( | # Refinement of individual xyz and b-factors every cycle with optimized weights (info: optimize_xyz_weight=true optimize_adp_weight=true makes the program take longer!); | ||
# Simulated annealing at 2nd and one before the last cycles; | # Simulated annealing at 2nd and one before the last cycles; | ||
# find (and remove if necessary) water molecules | # find (and remove if necessary) water molecules | ||
''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. | ''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 === | ||