[phenixbb] TLS in phenix.refine_gui

Pavel Afonine pafonine at lbl.gov
Sun Jan 11 10:11:30 PST 2009

Hi Nat,

- the file with TLS selections produced by TLSMD server is just a piece 
of parameter file. I usually take that file and grow it by adding some 
other parameters, such as main.number_of_macro_cycles, etc...

- I don't think it's a good idea to rely on file extensions... When you 
run phenix.refine from the command line you can give it a file with 
parameters and the name or extension of that file can be any. Why it's 
different in the GUI?

- I think a prompt for a parameter file should be right next to the PDB, 
data and CIF file fields in "Input data" section of phenix.refine GUI, 
since it's pretty often that users have their own set of custom parameters.


On 1/11/2009 9:19 AM, Nathaniel Echols wrote:
>> Is there a way to load the TLS groups, generated so kindly by TLSMD  
>> in old phenix format, into the new gui?  It would save a lot of  
>> typing.
> The file extension must be .eff or .param, otherwise the GUI won't be  
> able to figure out what kind of file it is.   Once this is done, there  
> are three ways to load it:
> 1. Make it a command-line argument when you launch phenix.refine_gui.   
> (the goal is for the GUI to take all the same arguments as the command- 
> line-only version - not sure if that made it into this installer, but  
> it'll definitely load any named files that it recognizes.)
> 2. Place the file in phenix/defaults/ in whatever you picked as the  
> project directory, and it'll be loaded on startup.  The next installer  
> will simplify this procedure.
> 3. Load it from the file menu.  This is more problematic, but should  
> be fine for tls groups.  There isn't a space for this in the "input  
> files" section of the window because these files are handled  
> differently than pdb files etc., and they're difficult to undo.  (this  
> is just a quirk of the way configuration is handled in the background.)
> I didn't realize that tlsmd would produce a file for phenix; I'll add  
> a button to that dialog window for loading these files unmodified.
> Nat
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