On Mon, Dec 20, 2010 at 7:43 AM, Luke Rice
I am trying to evaluate whether or not secondary structure restraints are going to help me with the refinement I am working on. When I ran in 'auto' mode, I noticed that by default phenix specifies several a-helices as 3_10. So, I would like to use an edited list of secondary structure restraints.
Interesting, usually it's the reverse problem (3_10 helices annotated as alpha) - but the annotation program can be a little twitchy. I had intended for this to be graphically editable, but now that I've checked I see there's no way to actually change the helix type in the GUI. Will fix that soon.
Can I specify this file in the GUI? (Like Joe Noel, I, too, have become soft). I looked in what I thought to be the obvious places and did not turn anything up.
You can just drag it into the main input file list. Any parameter file may be used this way, with the caveat that the GUI will not actually display the parameters it contains (but they will be incorporated into the final config file). For this reason I recommend against using complete .eff or .def files from command line runs, but the output of phenix.secondary_structure_restraints (or the edited version thereof) is pretty safe. Alternately, if you drag the parameter file onto the phenix.refine icon in the main GUI and release the mouse button, it should launch the phenix.refine GUI with all parameters in the file loaded in displayed in the GUI. (Since this isn't very obvious, I'll add a menu item somewhere to do the same thing less opaquely.) -Nat