[phenixbb] ncs

Maia Cherney chern at ualberta.ca
Tue May 5 14:14:19 PDT 2009

Thank you Nat, Pavel,

Actually, the NCS approaches a 3-fold crystallographic symmetry axis 
with 3 types of protein molecules plus 2 restraint groups for DNA molecules.

The result is the same with "optimize_wxc=true optimize_wxu=true" 
options, Rfree is going up without NCS by ~1.5%. Rwork is practically 
the same.

Should I increase the test set (now it's 5%)? or should I leave NCS=true 
for the final pdb?


Nathaniel Echols wrote:
> On May 4, 2009, at 6:48 PM, Maia Cherney wrote:
>> The resolution is 2.15 A. The NCS was always on during the refinement
>> until we got low R factors (19.2% and 21.2%). Then the NCS was turned
>> off for the final refinement and the R factors increased, which is
>> strange as they should be going down when you apply less restraints.
> This isn't necessarily true - regardless of which program you use to  
> refine, R-work isn't actually the refinement target, and minimization  
> algorithms aren't foolproof either.  When you remove the restraints  
> you are effectively decreasing the observation:parameter ratio, which  
> increases the risk of overfitting.  If nothing else I would expect the  
> gap between Rwork and Rfree to increase, but I've also seen both  
> increase when NCS restraints were removed.
> It may be possible that the NCS restraints are biasing your test set,  
> leading to the suspiciously low Rfree-Rwork gap, but I thought this  
> only applied when the NCS approached crystallographic symmetry, and  
> there's no such thing as fivefold crystallographic symmetry.   
> Hopefully someone else on the list can clarify this.
> -Nat
> -------------------
> Nathaniel Echols
> Lawrence Berkeley Lab
> 510-486-5136
> NEchols at lbl.gov
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