[phenixbb] ncs

Pavel Afonine PAfonine at lbl.gov
Mon May 4 18:53:25 PDT 2009


I see. I suggest to run two refinements:

- with NCS and "optimize_wxc=true optimize_wxu=true" options, and

- without NCS and with "optimize_wxc=true optimize_wxu=true".

This will make it weight-choice independent and so easier to understand. 
Otherwise, since NCS term is included in weights calculation, using or 
not using NCS may change the X-ray/Restrains weight which may have 
larger effects than using/not using NCS itself.

Pavel.


On 5/4/09 6:48 PM, Maia Cherney wrote:
> Hi Pavel,
> 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. 
> There are five restraint groups in the asym. unit.
>
> Maia
>
>
>
> Pavel Afonine wrote:
>   
>> Hi Maia,
>>
>> - I'm wondering why this puzzles you?
>>
>> - The gap Rfree-Rwork seems suspiciously small, although I can't tell 
>> without knowing the resolution.
>>
>> - Overall, better R-factors (Rwork, Rfree and Rfree-Rwork) mean that 
>> among many possible refinement strategies you have chosen the one that 
>> is better than the others.
>>
>> What is the resolution?
>> What are the R-factor  before using NCS?
>> What will be the R-factors after you turn NCS back off?
>>
>> Pavel.
>>
>>
>> On 5/4/09 12:27 PM, Maia Cherney wrote:
>>   
>>     
>>> Hi everybody,
>>> I am wondering why my final structure refined with NCS=True has lower  R 
>>> factors (19.2% and 21.2%) than without NCS by approximately 1.5%.
>>>
>>> Leo
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>
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