[phenixbb] Query re individual sites (real space)

Pavel Afonine pafonine at lbl.gov
Tue Dec 21 00:49:59 PST 2021

Hi Oli,

the code that does this is quite old and the logic behind it is 
described here:


I can look into glitches in your specific example if you send me all inputs.


On 12/20/21 12:58, Oliver Clarke wrote:
> Hi,
> While refining an X-ray structure using phenix.refine (v1.20-4444), I 
> get the attached table during real-space refinement of coordinates. 
> What are the criteria for selecting the correct weighting factor?
> I assumed it would be the delta between R/Rfree and/or the clash 
> score, but it doesn't seem to exactly match either in this table (and 
> the same for other iterations of refinement). Is it just incorrectly 
> writing the clash score in the "Accepted refinement result" line? 
> Shouldn't this match the line from the selected weight (here 0.125 so 
> should be 6.1, not 7.1)?
> Cheers
> Oli
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