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

Luke Rice luke.rice at utsouthwestern.edu
Mon Dec 20 11:23:30 PST 2010

Hi Nat,

I tried what you suggested (dragging my ss restraints file into the 
input area), and it does not seem to be working (i.e. my edited 
restraints do not show up; also the filename never appears in the box). 
I tried changing the fsuix to .eff or .def or .txt, none worked. If 
instead I drag my restraints file onto the phenix.refine icon, I get a 
warning about 'this application does not support the filetype ...'.

I assume that as usual I am doing something wrong. Any ideas?



Nathaniel Echols wrote:
> 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.)
> -Nat
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Luke M. Rice
Assistant Professor and
Thomas O. Hicks Scholar in Medical Research
Department of Biochemistry, ND10.300
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
phone: (214) 645-5931
email: Luke.Rice at UTSouthwestern.edu

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