When creating an NCS average map, Coot draws a box around the chain of
interest and averages the map inside that. Everywhere else is set to 0.
So inside the box, yes, one might expect the rms value to be a small
amount larger (considering points inside the box). However, most of the
ASU is set to 0, so overall, the rms of the average map will be
considerably less.
Bottom line is that y.y is difficult to calculate unless you cut the map
back to the box values - I suppose that the output of Coot and mapmask
would help there, although for clarity you would have to explain how
sigma is derived (it is often opaque, it seems to me).
Paul.
On 22/12/10 23:37, Dale Tronrud wrote:
> The "12 sigma" I want to put in the paper is from the Fo-Fc map
> where the rms is more comparable to a sigma. You are right that
> e/A^3 is the best "units" for describing density but for my water
> creation criteria I would like to say "higher than x.xx e/A^3 in
> the difference map which is y.y sigma."
>
> I would never attempt to ascribe statistical meaning to the
> rms of a 2Fo-Fc map. I chose to describe my confusion about
> its calculation in Coot for ncs averaged maps because I could
> describe my puzzlement more easily. With a Fo-Fc style map you
> expect the "sigma" of the peaks to get bigger after averaging
> and you have to argue how much larger is plausible. For a
> 2Fo-Fc style map the density should not get much higher, in
> terms of rms, with averaging and yet in Coot it does. My guess
> is that the calculation is done the same way for both types of
> maps.
>
> Dale
>
> On 12/22/10 15:08, Phil Evans wrote:
>> Why do you want to quote "sigma" level anyway? It's more or less meaningless for the reasons you give. Stick to e/A^3
>>
>> </flame>
>> Phil
>>
>> On 22 Dec 2010, at 22:02, Dale Tronrud wrote:
>>
>>> Hi,
>>>
>>> I have a crystal structure at 3A resolution with six copies in the
>>> asu. When I average the map over the ncs I find that the original
>>> 2Fo-Fc style map has a sigma of 1.5 at 0.3 e/A^3. When I adjust the
>>> contour level of the averaged map to match, by eye, the level of the
>>> unaveraged map I find them equivalent at a sigma of 2.6 at 0.28 e/A^3.
>>> These results imply that the "sigma" level of the original map was
>>> 0.2 e/A^3 and the averaged map was 0.11 e/A^3.
>>>
>>> The "sigma" of a 2Fo-Fc style map is not an estimate of uncertainty,
>>> of course, because nearly everything in the map is signal. It is
>>> just a measure of the variability of the signal, i.e. the rms. With
>>> averaging the signal should be preserved and the noise reduced, but
>>> the noise of a 2Fo-Fc map is small compared to the signal. How is
>>> it that the rms of my averaged map drops to half of the unaveraged
>>> value and yet the electron density looks about the same when contoured
>>> at the same e/A^3 (0.3 vrs 0.28)?
>>>
>>> I guess the real question is, how does Coot calculate the "sigma"
>>> of an averaged map? You can't calculate the rms over the asymmetric
>>> unit because the asymmetric unit is many millions of unit cells in
>>> size (and hugely variable depending on small changes in the ncs
>>> operators).
>>>
>>> The problem at hand is that I want to quote the sigma level I
>>> insisted upon when creating water molecules and think it will sound
>>> weird if I say I used a value of 12, which I did. The numbers just
>>> don't seem right to me so I'd like a little reassurance.
>>>
>>> Dale Tronrud
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