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Phenix: Difference between revisions
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== Example == | == Example == | ||
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 | ||
| Line 11: | Line 11: | ||
This will do the following: | This will do the following: | ||
# | # Rigid body refinement first cycle only (MZ protocol = VERY high convergence radius); | ||
# | # Refinement of individual xyz and b-factors every cycle with optimized weights; | ||
# | # Simulated annealing at 2nd and one before the last cycles; | ||
If some ligand in model.pdb is unknown, phenix.refine will complain: | |||
Sorry: Fatal problems interpreting PDB file: | |||
Number of atoms with unknown nonbonded energy type symbols: 18 | |||
Please edit the PDB file to resolve the problems and/or supply a | |||
CIF file with matching restraint definitions, along with | |||
apply_cif_modification and apply_cif_link parameter definitions | |||
if necessary (see phenix.refine documentation). | |||
Also note that phenix.elbow is available to create restraint | |||
definitions for unknown ligands. | |||
In that case, just running | |||
phenix.elbow model.pdb --do-all --output=all_ligands | |||
will produce all_ligands.cif, which may be fed to phenix.refine by | |||
phenix.refine model.pdb data.mtz all_ligands.cif ... | |||
== See also == | |||
[http://www.phenix-online.org/ Phenix home page] | [http://www.phenix-online.org/ Phenix home page] | ||