[phenixbb] optimize phenix

[Ralf W. Grosse-Kunstleve]

> Is it any tools in the phenix that could optimize the secondary
> structures alone in the pdb?

We don't have direct support for secondary structure restraints
(although this came up quite often already).
Using external tools you could prepare a file with "custom bond"
restraints as described in the phenix.refine documentation. Note
that the "slack" parameter is meant for hydrogen bond restraints,
which I assume you want to use.

Ralf