On Jun 20, 2013, at 12:20 PM, Dale Tronrud <[email protected]> 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 <[email protected]> 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
