[phenixbb] question on the missing fobs filled maps

Pavel Afonine pafonine at lbl.gov
Mon Nov 8 15:40:21 PST 2010

  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)?


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