On Wed, Apr 7, 2010 at 4:38 PM, r n
I wanted to do low resolution rigid body refinement with secondary structural restrain. I have not seen any command or information in the phenix document?
Okay, finally writing documentation now. Sorry! There isn't actually a method for combining rigid body refinement with secondary structure information yet; it would probably be a day or two of work for Pavel or me. However, the "morph" option on AutoBuild may do a better job at moving pieces of that size into place. (And there are probably other programs which I haven't used that do something similar.) You can use the secondary structure restraints with simple coordinate refinement (strategy individual_sites), by adding "main.secondary_structure_restraints=True" to the command-line (there is a corresponding button in the GUI, but only if you have the alpha-test mode turned on). Everything else is (in theory) automatic, but if you aren't using hydrogens, add "h_bond_restraints.substitute_n_for_h=True" as well, just to be safe. -Nat