[phenixbb] optimize phenix

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Mon Jan 4 08:56:52 PST 2010

> 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.


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