[phenixbb] question on the missing fobs filled maps

fn1 at rice.edu fn1 at rice.edu
Mon Nov 8 17:01:07 PST 2010

I am interesting in that at what completeness of the dataset, will one  
use the missing fobs filled map for model building confidently without  
too much bias included?


引用 Pavel Afonine <pafonine at lbl.gov>:

>  Hi Fengyun,
>> I have two datasets, one of which the completeness is only about  
>> 81%, the other one is even lower, about 45%.
>> The resulting "missing fobs filled map" is much better than the  
>> unfilled map in the loop region. I read one file of Pavel on the  
>> fact of maps, the concern of using missing fobs filled map is that  
>> the risk of the mdoel bias.
>> My question is that could the missing fobs filled map be used for  
>> the model building?
> a "missing fobs filled map" is always computed using 100% set of  
> reflections. For example, if your original dataset is 81% complete,  
> that means the "missing fobs filled map" is computed using existing  
> 81% of data plus 19% of reflections to fill the gap. These 19% are  
> DFc. In extreme case of 0% or close to 0% data completeness this  
> because just Fcalc map.
> Therefore it's clear that "missing fobs filled map" map should be  
> used with care, and it is a good idea to look at both maps (one  
> computed using original data, and another one using the data where  
> missing reflections filled in with DFc).
> "filled" maps can produce a clearer picture and may disambiguate  
> hard-to-interpret density, while may be biased. Regular maps may be  
> of poorer quality (due to data incompleteness), but are not model  
> biased due to "filling" (although may be model biased caused by  
> other reasons than "filling").
> Given data completeness you have I wouldn't use "filled" maps.
> I'm wondering what Refmac does in this case (as far as I know it  
> always outputs "filled" map)?
> Pavel.
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