[phenixbb] WAS: changing TLS groups mid refinement
PAfonine at lbl.gov
Mon May 17 12:40:33 PDT 2010
> This has been discussed before. For a start look at French and Wilson
> (French G.S. and Wilson K.S. Acta. Cryst. (1978), A34, 517.)
do they demonstrate the benefits of using these data in refinement (see
below)? Well, I guess I need to re-read it again.
> Fobs < 0 is not possible, but Fobs = 0 clearly conveys some
> information (i.e. the reflection is weak). Simply deleting the data is
> the worst case scenario where you remove any information content on
> that reflection during refinement. I'm surprised that this would even
> need further exposition, especially in light of the community tendency
> to use higher outer-shell Rsymms (50-60%) where a significant
> proportion of the data would be expected to be weak and therefore
> subject to risk of arbitrary cutoff by phenix.refine. If I/sigI = 2 (a
> not uncommon outer shell criterion) then a decent proportion of the
> data might have I<0, and this data is really there and weak and not
> the imagination of the processing program.
I'm all with you: yes, more data is better.
Although, I repeat my original question:
Did anyone demonstrate that:
"refinement with Fobs=0" vs "refinement with Fobs>0" results in :
- noticeably better map, so you can find more details, explain more
- noticeably better model,
- anything else visibly better ?
If so then I agree it is worth spending time on implementing it.
However, if it's just theoretically/esthetically nice to have it (as
many other things, like better than Flat bulk solvent model), but the
benefits are not really clear - then I would still have it in my todo
list (since it's good in general) but with much lower priority.
Yes, treating properly negatives and zeros is theoretically good. There
is even a paper with myself being a co-author that touches on it.
But for practical considerations it's all about the ratio "time invested
into implementing it vs benefits obtained as result".
> Does phenix.refine enforce an I<=0 cutoff too ? It certainly behaves
> as if it does.
phenix.refine does not have intensity based X-ray refinement targets and
therefore phenix.refine does not use intensities in refinement. Although
it accepts input reflection files with intensities which it then
converts to amplitudes for all subsequent purposes.
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