[phenixbb] nucleic acid secondary structure restraint sigmas

Dyda dyda at ulti.niddk.nih.gov
Fri Mar 23 09:55:57 PDT 2018


Does anyone one whether is it possible (and if so how)
to change the target sigmas of the H-bonds restraining base pairs?

It seems that base pair restraints can do several things:

        base_pair {
          enabled = True
          base1 = chain 'C' and resid 21
          base2 = chain 'D' and resid 5
          saenger_class = 19
          restrain_planarity = False
          planarity_sigma = 0.176
          restrain_hbonds = True
          restrain_hb_angles = True
          restrain_parallelity = True
          parallelity_target = 0
          parallelity_sigma = 0.0335

What I'd like to know whether the restrain_hbonds and  restrain_hb_angles sigmas can be adjusted.
Or is it the case that parallelity_sigma is doing what I'm looking for?


Fred Dyda, Ph.D.                       Phone:301-402-4496
Laboratory of Molecular Biology        Fax: 301-496-0201
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