[phenixbb] Secondary structure restraints - where to specify file using GUI?

Nathaniel Echols nechols at lbl.gov
Mon Dec 20 08:09:59 PST 2010

On Mon, Dec 20, 2010 at 7:43 AM, Luke Rice <luke.rice at utsouthwestern.edu> wrote:
> 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.)


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