[phenixbb] WAS: changing TLS groups mid refinement

Pavel Afonine PAfonine at lbl.gov
Mon May 17 08:47:15 PDT 2010

Hi Ed,

I agree I was too generous in my statement and you promptly caught it, 

phenix.refine does catch and deal with clearly nonsensical situations, 
like having Fobs<=0 in refinement. So, saying "phenix.refine does not 
use any data cutoff for refinement" was not precise, indeed. In 
addition, phenix.refine automatically removes Fobs outliers based on 
R.Read paper.

I don't see much sense having a term (0-Fcalc)**2 in least-squares 
target or equivalent one in ML target. Implementing an intensity based 
ML target function (or corresponding LS) would allow using Iobs<=0, but 
this is not done yet, and this is a different story -  your original 
question below was about Fo (Fobs).

Do you have rock solid evidence that substituting missing (unmeasured) 
Fobs with 0 would be better than just using actual set (Fobs>0) in 
refinement? Or did I miss any relevant paper on this matter? I would 
appreciate if you point me out. Unless I see a clear evidence that this 
would improve things I wouldn't waste time on implementing it. 
Unfortunately I don't  have time right now for experimenting with this 


On 5/17/10 6:52 AM, Ed Pozharski wrote:
> On Fri, 2010-05-14 at 15:35 -0700, Pavel Afonine wrote:
>> phenix.refine does not use any data cutoff for refinement.
> So was the Fo>0 hard-wired cutoff removed?  I don't have the latest
> version so I can't check myself.
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