[phenixbb] Parameters in "reference_model" during "real space refinement"

Oleg Sobolev osobolev at lbl.gov
Mon Nov 8 14:34:52 PST 2021

Hi Nicolas,

   I would be interested in understanding more the exact meaning of the
> options related to "reference model" when doing "real space refinement" (in
> https://phenix-online.org/documentation/reference/real_space_refine.html):
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
> information?
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.

Best regards,
Oleg Sobolev.

> Thanks,
> Best,
> Nicolas
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