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! Pavel.