[phenixbb] Parameters in "reference_model" during "real space refinement"
osobolev at lbl.gov
Mon Nov 8 14:34:52 PST 2021
I would be interested in understanding more the exact meaning of the
> options related to "reference model" when doing "real space refinement" (in
Given that reference model restraints are dihedral restraints derived from
reference model and applied to refined model:
> - hydrogens = False
> Include dihedrals that include hydrogen atoms
> - main_chain = True
> Include dihedrals formed by main chain atoms
> - side_chain = True
> Include dihedrals formed by side chain atoms
> - fix_outliers = True
> Try to fix rotamer outliers in refined model
> - strict_rotamer_matching = False
> Make sure that rotamers in refinement model matches those in reference
model even when they are not outliers
> - auto_shutoff_for_ncs = False
> Do not apply to parts of structure covered by NCS restraints
> - secondary_structure_only = False
> Only apply reference model restraints to secondary structure elements
(helices and sheets)
> It is a bit unclear what setting each of them to "True" would exactly
> imply or what the difference between them are. Does anyone have more
In the majority of cases default parameters should be good.
The paper on this is:
Use of knowledge-based restraints in phenix.refine to improve
macromolecular refinement at low resolution. J. J. Headd, N. Echols, P. V.
Afonine, R. W. Grosse-Kunstleve, V. B. Chen, N. W. Moriarty, D. C.
Richardson, J. S. Richardson, P. D. Adams. Acta Crystallogr D Biol
Crystallogr 68, 381–390 (2012). doi:10.1107/S0907444911047834
Please let us know if you have more questions.
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