[phenixbb] Clearing old NCS group definitions

Nathaniel Echols NEchols at lbl.gov
Wed Dec 9 03:54:50 PST 2009

On Dec 8, 2009, at 11:00 PM, John Pascal wrote:
> I am using NCS restraints in phenix.refine, and I am defining the restraints in
> a parameter file that I read into the GUI interface. After modifying the ncs
> parameters file, I see in the log file that phenix.refine has used the updated
> NCS groups, but also retains the old restraints settings.  Therefore, the
> number of NCS groups doubles each time I make an edit.  Is there a way to erase
> the previous NCS restraints?

There are some quirks in the way the GUI handles parameter files that are input as separate files - specifically, they will not overwrite existing parameters.  (There is a good reason for this, but I can't remember it at the moment.)  In general, I don't recommend setting parameters this way, because the parameters are used internally to draw controls and there are some built-in limitations to how flexibly it can handle different sources.  Editing files externally that are used by the GUI is also problematic.  I would recommend using the built-in graphical NCS restraint editor, especially since this will allow you to save default restraints so you don't have to re-load them in the future.  If you want it to start with the restraints in your file, you have two options:

1. Drag-and-drop the parameter file onto the phenix.refine button in the main GUI - this will open a new window with the NCS restraints already loaded.  Alternately, if you start phenix.refine_gui from the command line, add the file to the argument list.  (In general, these are the safest methods for supplying parameters from a separate file.)

2. Copy the file to <project_dir>/phenix/defaults/ncs.params, and it will be loaded whenever the GUI starts.

> I see that the restraints are accumulating in the project_data/*.eff files.  Are
> those read in by default on consecutive runs?

No, the only time these are used after the job is complete is when you restore the job in the main GUI.


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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