On Jun 20, 2013, at 12:20 PM, Dale Tronrud <[log in to unmask]> wrote:
> If you are refining against F's you have to find some way to avoid
> calculating the square root of a negative number. That is why people
> have historically rejected negative I's and why Truncate and cTruncate
> were invented.
>
> When refining against I, the calculation of (Iobs - Icalc)^2 couldn't
> care less if Iobs happens to be negative.
But we know that Is can't be negative. Using (Iobs - Icalc)^2 does not incorporate that bit of physics, and it implicitly assumes a Gaussian distribution for the Is, which is impossible for a variable that is positive semi-definite. Refining against (Iobs - Icalc)^2 is mathematically equivalent to shifting every I by the most negative I and refining against that, a crude baseline correction that I doubt most people would consider valid. Transforming the data to Fs at least makes the Gaussian assumption plausible, and I always assumed that was one main reason for working with Fs (since all the refinement programs assume Gaussians).
> As for why people still refine against F... When I was distributing
> a refinement package it could refine against I but no one wanted to do
> that. The "R values" ended up higher, but they were looking at R
> values calculated from F's. Of course the F based R values are lower
> when you refine against F's, that means nothing.
R-values also implicitly assume a Gaussian, right?
>
> If we could get the PDB to report both the F and I based R values
> for all models maybe we could get a start toward moving to intensity
> refinement.
>
> Dale Tronrud
>
> On 06/20/2013 09:06 AM, Douglas Theobald wrote:
>> Just trying to understand the basic issues here. How could refining directly against intensities solve the fundamental problem of negative intensity values?
>>
>>
>> On Jun 20, 2013, at 11:34 AM, Bernhard Rupp <[log in to unmask]> wrote:
>>
>>>> As a maybe better alternative, we should (once again) consider to refine against intensities (and I guess George Sheldrick would agree here).
>>>
>>> I have a simple question - what exactly, short of some sort of historic inertia (or memory lapse), is the reason NOT to refine against intensities?
>>>
>>> Best, BR
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