Phenix: Difference between revisions

269 bytes added ,  17 July 2010
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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
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 ...


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 ==
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