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 <[log in to unmask]> 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.
>>
>>
>
|