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

Engin Ozkan eozkan at stanford.edu
Thu Mar 25 09:19:31 PDT 2010

  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.


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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> 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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100325/136852fe/attachment-0003.htm>

More information about the phenixbb mailing list