phenix.refine
Contents
1. Introduction
phenix.refine is the macromolecular refinement engine of the Phenix suite. It features
- Individual as well as grouped B factor refinement
- Anisotropic or isotropic+anisotropic B factor refinement
- TLS refinement
Many other options/features are highlighted in the manual
phenix.refine is typically run as
phenix.refine mypdb.pdb mydata.mtz
or (when a parameter file is present) as
phenix.refine lysozyme_refine_002.def
2. Know Bugs
None
3. FAQ
3.1. How does one pick waters?
Specify the keyword ordered_solvent=True on the command line, or change this variable in the .def file.
3.2. What does the line "REMARK twinned : True" in the output PDB file mean?
This indicates that the data might be twinned. Please run
mmtbx.xtriage mydata.mtz <options>
to get more details. See also mmtbx.xtriage for more details.
4. Discussion
4.1. Refinement scenarios
4.1.1. standard refinement, all defaults
phenix.refine mydata.mtz mymodel.pdb
4.1.2. refinement and water picking
phenix.refine mydata.mtz mymodel.pdb ordered_solvent=True