[phenixbb] Where to find optimized wxc_scale/wxu_scale weighting factors after optimization
pafonine at lbl.gov
Thu Aug 12 13:05:11 PDT 2010
>>> 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
> 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
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