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Phenix: Difference between revisions
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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 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 \ | ||
ordered_solvent=True | |||
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 (warning: optimize_wxc=true optimize_wxu=true makes the program use '''much''' more time!) | # 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; | ||
# 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. | ||
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will produce all_ligands.cif, which may be fed to phenix.refine by | will produce all_ligands.cif, which may be fed to phenix.refine by | ||
phenix.refine model.pdb data.mtz all_ligands.cif ... | phenix.refine model.pdb data.mtz all_ligands.cif ... | ||
If no PDB file for a ligand is available, its SMILES string should be input to phenix.elbow, and phenix.ready_set should run to generate the link records (???), using phenix.elbow's CIF file. | |||
== Constraints and restraints in real space == | |||
=== [http://www.phenix-online.org/documentation/refinement.htm#anch32 Hydrogens] === | |||
Use phenix.ready_set to add hydrogens to your PDB file, and (except at ultra-high resolution) the riding hydrogen model in phenix.refine (this is the default so you do not have to specify anything). | |||
phenix.ready_set internally uses phenix.elbow for ligands and phenix.reduce for the protein. phenix.pdbtools can also add hydrogens (FIXME: what are the differences?). | |||
Hydrogens should not be used in NCS and TLS groups - it might be a good idea to add <font face="Courier"> and not (element H or element D)</font> to all selection strings. | |||
=== Occupancy === | === Occupancy === | ||
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== reciprocal space == | == Constraints and restraints in reciprocal space == | ||
=== TLS === | === TLS === | ||