[phenixbb] WAS: changing TLS groups mid refinement

Pavel Afonine PAfonine at lbl.gov
Mon May 17 12:40:33 PDT 2010

Dear Phil,

> 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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