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Phenix: Difference between revisions
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=== basic usage === | === basic usage === | ||
phenix.refine model.pdb data.mtz | phenix.refine model.pdb data.mtz | ||
Here "data.mtz" is your reflection data file. PHENIX automatically recognizes most of the known file formats, so it can be MTZ, CNS or ... | |||
=== 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 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 | ||
This will do the following: | This will do the following: | ||
# 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 (warning: optimize_wxc=true optimize_wxu=true makes the program use '''much''' more time!) | ||
# 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. | ''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: | ||
Sorry: Fatal problems interpreting PDB file: | Sorry: Fatal problems interpreting PDB file: | ||
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} | } | ||
== TLS == | === Secondary structure restraints === | ||
phenix.refine model.pdb data.mtz main.secondary_structure_restraints=true | |||
== reciprocal space == | |||
=== TLS === | |||
* run your model through TLSMD server to identify TLS domains (it will produce PHENIX friendly TLS groups selections); | * run your model through TLSMD server to identify TLS domains (it will produce PHENIX friendly TLS groups selections); | ||
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} | } | ||
== Rigid body == | === Rigid body === | ||
example for file rigid_body.def defining 2 rigid bodies: | example for file rigid_body.def defining 2 rigid bodies: | ||
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rigid_body = chain 'L' or chain 'M' | rigid_body = chain 'L' or chain 'M' | ||
} | } | ||
== Atom selection == | |||
e.g. | |||
phenix.refine model.pdb data.mtz refine.sites.individual="not (chain A and resseq 123:156)" | |||
== Switching off specific interactions == | == Switching off specific interactions == | ||