[phenixbb] ncs restraint

Pavel Afonine PAfonine at lbl.gov
Mon May 25 15:41:09 PDT 2009

Hi Engin,

since the model gets improved during refinement (hopefully), it is a 
good idea to update NCS restraints based on improved model, so the 
default behavior.

The use of NCS restraints in phenix.refine is explained in the manual:

I admit that the automatic NCS determination has a room for improvement, 
but once again: ideally it should be done fully automatically and be 
updated as model gets improved. It is in my list...

As it is now it's always good to check the automatic choice (as Ralf 


On 5/18/09 3:33 PM, Engin Ozkan wrote:
> Also, don't forget to add ncs.find_automatically=false
> I have run many runs with NCS defined with proper syntax, just to be 
> overwritten by NCS derived automatically by phenix, until I realized 
> what was happening. I have always thought that if I define the NCS 
> restraints, phenix should follow it, not try to "improve" upon it.  What 
> is the reason for this default behavior?
> Engin

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