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

[Coudray, Nicolas]

Hi,


   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):

  *   hydrogens = False
  *   main_chain = True
  *   side_chain = True
  *   fix_outliers = True
  *   strict_rotamer_matching = False
  *   auto_shutoff_for_ncs = False
  *   secondary_structure_only = False

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?


Thanks,

Best,

Nicolas



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