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

Coudray, Nicolas Nicolas.Coudray at nyulangone.org
Mon Nov 8 15:05:27 PST 2021

Hi Oleg -

Thanks a lot for the detailed answer!



From: Oleg Sobolev <osobolev at lbl.gov>
Sent: Monday, November 8, 2021 5:34 PM
To: Coudray, Nicolas
Cc: phenixbb at phenix-online.org
Subject: Re: [phenixbb] Parameters in "reference_model" during "real space refinement"


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<https://urldefense.com/v3/__https://phenix-online.org/documentation/reference/real_space_refine.html__;!!MXfaZl3l!PtWqAe3o6W8tEknDNzye9dt1zcMId4s7Fwi7FlTHKnwm_LpnuvvbbT43oWcVljUKnzq_q53I$>):

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.




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