[phenixbb] low resolution secondary structure refinement

[Ralf W. Grosse-Kunstleve]

> I'm not sure to what extent this is true.  Ralf, what would be the effect of
> those extra H-bonds when running torsion angle dynamics?  Will they be used
> in the rigidity analysis, or will they just behave as they would in
> cartesian dynamics?

The rigidity analysis excludes bonds with a slack != 0; they will
only be maintained as restraints.
All bonds with slack == 0 are treated the same, no matter how they
were defined (cif or custom or any other way).
Ralf