[phenixbb] Implementation of French & Wilson data correction?

Pavel Afonine pafonine at lbl.gov
Mon Feb 28 17:31:31 PST 2011

  Hi Keitaro,

> A little off-topic, but will phenix implement MLI (maximum likelihood
> intensity target)?

eventually. The formulas are there, someone just needs to get enough of 
motivation to spend a couple of days and code them thus making available 
in phenix.refine.
Once this is done, then there will be another set of troubles to deal with:
- what to use to compute R-factors: Iobs or Fobs? If Fobs, then in turn 
you will go back to the original problem of converting I to F. If Iobs, 
then I bet a number of people will scream that they want to see the 
R-factors computed the "usual way" (using Fobs, that is).
- Same questions about computing the maps.

> I heard that MLI target gives a good result because MLI handles
> negative intensities naturally.

"Good" compared to what? How you evaluate that one is better than the 
other in this case? Obviosuly, you wouldn't be able to use the R-fators 
as the criteria. I guess I know how, but I'm not aware that anyone has 
ever done it (another little project for someone enthusiastic).

Overall, I conclude quoting one of my favorite papers:

"The choice of refinement against F**2 or F has generated more 
discussions than it probably warrants. (...)"

David Watkin
"Structure refinement: some background theory and
practical strategies"
J. Appl. Cryst. (2008). 41, 491–522

All the best!

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