I remember this. At least from running phenix.refine on command-line, there is a parameter called ncs.find_automatically. It is "True" by default. I remember spending several days trying to change the NCS selections, until I found about this parameter. So, unless you change this parameter to "False", your input is always written over. I am not sure where this might be in the GUI, but it could be the culprit. To see if this is the case, in the Refinement Settings tab, go to All Parameters -> View all settings. There, check under parameters -> refinement -> ncs. You can also find it in the refine_??.eff file, just search for this parameter.

Best,
Engin


On 3/25/10 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:

1. I set the NCS groups definition in the GUI to go from residues 35:445 , 
2. I check that using the view pick . Everything looks fine 
3. I click the Green update and exit button
4. I look at the ncs.params file in the project defaults directory and it indeed reflects the changes . 
5. 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.

Any idea why I cannot get the gui run refinement to remember my ncs definitions.

Thanks in advance

Hari

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-- 
Engin Özkan 
Post-doctoral Scholar 
Laboratory of K. Christopher Garcia 
Howard Hughes Medical Institute 
Dept of Molecular and Cellular Physiology 
279 Campus Drive, Beckman Center B173 
Stanford School of Medicine 
Stanford, CA 94305 
ph: (650)-498-7111

_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb

-- 
Engin Özkan 
Post-doctoral Scholar 
Laboratory of K. Christopher Garcia 
Howard Hughes Medical Institute 
Dept of Molecular and Cellular Physiology 
279 Campus Drive, Beckman Center B173 
Stanford School of Medicine 
Stanford, CA 94305 
ph: (650)-498-7111