[phenixbb] phenix and weak data

Pavel Afonine pafonine at lbl.gov
Mon Dec 10 13:17:46 PST 2012


>>   I mean not an R-factor improvement by a fraction of a percent or
>> "cosmetics" like this, but a case where it is demonstrated that using
>> it allowed more model to be built, or showing two maps side-by-side
>> obtained without and with weak data where the latter would
>> significantly be more useful (not just appears more pleasant after
>> tweaking contouring thresholds to show the case favouritely).
> If the standard is that improvements in crystallographic refinement
> process/algorithms only are justified when "more model can be built",
> then many algorithm improvements should be abolished.  TLS refinement is
> a widely accepted strategy, although it never (to my knowledge) was
> really demonstrated that it allows you to magically see something new in
> the density that was not there before.  You are right that a lot of
> things we do to optimize crystallographic models do not change electron
> density in a dramatic way.  You are absolutely wrong in your assertion
> that improvements of the accuracy of model parameters are pointless.

same remark goes here about efficiency of email communication (see 
previous email).

The point was that one always needs to draw a line between pedanticism 
and practicality. Otherwise we would be all going back from FFT to 
direct summation in Fcalc and gradients calculation, as that would 
surely improve R-factors by 0.5-1% or so in some cases through improving 
the accuracy of refined model parameters.

All the best,

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