Hi Jay,
there have been a few discussions about sigma/rms levels, absolute
values (e/A*3), significance levels etc on ccp4bb. See e.g.
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which are the ones I could find again (I'm sure there are others).
One example: imagine you would know the true value of a distribution,
say on 17 points. You then start to model it (this corresponds to your
initial stages of refinement). After some cycles, you end up with a
model you're happy with.
It could look like this:
point true start end
-----------------------------
1 1.0 1.1 1.00
2 1.1 1.2 1.10
3 1.5 1.4 1.52
4 2.0 2.3 2.01
5 2.7 2.9 2.72
6 3.0 3.5 3.02
7 4.0 4.2 4.04
8 6.0 6.3 6.04
9 9.0 10.0 9.09
10 6.0 6.3 6.04
11 4.0 4.2 4.04
12 3.0 3.5 3.02
13 2.7 2.9 2.73
14 2.0 2.3 2.01
15 1.5 1.4 1.52
16 1.1 1.2 1.10
17 1.0 1.1 1.00
Now plot those distributions (see attached file) and calculate
mean/sigma of the differences (between the current model and the true
values):
start-true : <mean> = 0.2471 with sd = 0.2476
end-true : <mean> = 0.0235 with sd = 0.0219
You will see that point 9 always corresponds to a '3 sigma' difference
peak - even if your model at the end is pretty much perfect (R-factor
at the beginning is 9% and at the end down to 1%). Just because a
distribution will always give you a mean and a sigma it doesn't mean
that you need to chase after those '3 sigma' peaks forever.
At least that is how I visualise the sigma/rms/electrons issue for me
...
Cheers
Clemens
On Wed, May 19, 2010 at 12:13:54AM +0100, Jay Pan wrote:
> Hello Everyone,
>
> I have a reasonably well fitted electron density map through molecular replacement. However, there is always some red region left no matter how hard I tried when the mtz file is loaded into Coot. Is this because my model is still not good enough or it???s natural to most model fittings. In another word, should I be worried about the red region? Thanks in advance.
>
> Jay
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