[phenixbb] project defaults ncs.params not read or overridden/overwritten by GUI?

Nathaniel Echols NEchols at lbl.gov
Thu Mar 25 07:20:43 PDT 2010

On Mar 25, 2010, at 3:58 AM, hari jayaram wrote:
> Hi I am quite sure I am doing something wrong , but the refinement seems to always re-determine the NCS definitions despite it being set in the ncs.params file in the project defaults directory.
> Here is what I did:
> 	• I set the NCS groups definition in the GUI to go from residues 35:445 , 
> 	• I check that using the view pick . Everything looks fine 
> 	• I click the Green update and exit button
> 	• I look at the ncs.params file in the project defaults directory and it indeed reflects the changes . 
> 	• I start the refinement from the GUI and the ncs section seems to have been reset to 26:450 .  I even tried adding the ncs.params file to the Input files section, but to no avail. The ncs seems to always get re-determined and I end up getting an excessive distance stoppage of refinement. I even made sure I dont have the Find NCS restraints automatically button checked.

Not sure what's happening, but it looks like a bug - I'll try running something when I get into lab.  Could you please send me (not the list) the .eff file written out by the GUI?  (e.g. PROJECT/phenix/project_data/refine_1.eff, or something similar.)  Also, a simple test: set up the refinement, then click the Save button, and send me the file that it writes.

A possible fix: close the phenix.refine GUI, open a new window, add ncs.params to the input files (and make sure the find automatically option is unchecked).  Does this keep the groups you've set?

Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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