Eleanor, Do you have a rationale for assuming a lower uncertainty on the surface than in the core? I ask this because I did once look at the variation of the local RMSD of a difference Fourier, i.e. w(mFo-DFc) with w=2 for acentrics, w=1 for centrics, and I didn't find any obvious correlation with the location of the protein/solvent regions. The variation seemed to be just random and pretty well what one would expect given the sample size of the locally-defined region used to compute the uncertainty.
Cheers -- Ian On Mon, Apr 26, 2010 at 9:42 AM, Eleanor Dodson <[email protected]> wrote: > I am a bit out of touch with the discussion, and this may have been > mentioned already. > It is important to remember that Sigma is an OVERALL value for the whole > map, whereas one is looking for local solutions when fitting any density. > Stuff on the surface of the molecule ought to be contoured at a lower level > than in the ore, and this applies to protein as well as waters. > > Eleanor > > > Ed Pozharski wrote: >> >> On Wed, 2010-04-21 at 17:21 -0700, James Holton wrote: >>> >>> The "0.3% chance" of a peak being above 3 "sigmas" assumes that the >>> histogram of electron density values is Gaussian. It is not! In fact, it >>> is a funny-looking bimodal distribution (the peaks are protein and solvent >>> regions). >> >> Indeed! That's why it is a "bizarre" argument. In fact, standard >> deviation is rather meaningless unless one is dealing with "univariate" >> distribution. For bimodal distributions, changes of standard deviation >> are uninterpretable (without looking at the distribution, that is) since >> they can be due to both shifts and redistribution. >> >> Cheers, >> >> Ed. >> >> >
