[phenixbb] Where to find optimized wxc_scale/wxu_scale weighting factors after optimization

Pavel Afonine pafonine at lbl.gov
Thu Aug 12 13:05:11 PDT 2010

  Hi Yarrow,

>>> I was given these statistics in the pdb header:
>>>           Rwork   Rfree  Bonds  Angles
>>> start  .1588    .1838   .007  1.235
>>> end      .1454  .1780   .016  1.601
>>> (1.37 A resolution)
>> Looks ok. Did you update solvent using "ordered_solvent=true"? Did you
>> remember to add have H atoms to your structure?
> Thanks Pavel,
> No, I did not have these turned on.  It appears that
> "ordered_solvent=true" is essentially a water checker in later stages of
> refinement (correct me if I am wrong).  I will try turning this on.

refinement means changing your structure, and changing the structure 
means some map improvement. Since solvent is added using the maps 
(mFo-DFc and 2mFo-DFc) it is a good idea to re-check it (solvent) once 
the maps are updated. The result of such re-check may be some more good 
water added, or removing some wrong waters originally added to noise 
density peaks.

> What are the advantages of adding H atoms if you are not going to refine
> them?  (Bear with me--this is my first structure).

See pages from 27 here:


Let me know if it is still not entirely clear why you would need to use 
H-atoms in refinement.

After updating water and adding H atoms the R-factors may drop by 1-3%.

>>> 1.  I would like to find the optimized weighting factors in the log file
>>> but cannot.  Instead I find the following (pasted below).
>> I'm wondering why you are trying to find them? It is such a technical
>> thing that changes from macro-cycle to macro-cycle...
> I was attempting to use the best weighting factors in subsequent rounds of
> refinement so that I did not have to optimize each time (because it takes
> a long time to run).  Is this a good strategy?

I see. Although you can do it, it is good to keep in mind that these 
values can change between refinement runs. You can get this value for 
coordinate refinement and unfortunately this values is not printed out 
for ADP refinement (because of a formatting bug that I keep forgetting 
to fix).

Good luck!

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