At the risk of deafness from bees in bonnet (not to mention flogging
dead horses) ...
... the rms value of a "Fobs"-type map which represents the actual
structure (eg 2mFo - DFc) is _not_ an assessment of the "noise" level
of the map.
The rms value of a perfect map of this type is function of the
sharpness of protein features (which depends on the resolution & the B-
factors) and the solvent content (imagine the different rms levels of
the same molecule density placed in a cell with 40% solvent compared
to one with 80% solvent), and is not much related to the error.
The rms value is useful in ranking peaks in a difference map, but
even then if you imagine a near perfect difference map (we can dream),
close to zero density everywhere, there will still be peaks > 3 rms,
but they are not necessarily significant.
(yawn)
Phil
On 30 Jul 2008, at 12:58, P K wrote:
Thank you, Paul and Hidong, for your explanations. Here is another
way of looking at it (kindly provided by Ronald Stenkamp).
===
Think of the electron density as a 3-dimensional function with an
average value of 0.0 (This is true if you have not included an F000
reflection, and it's true of difference electron density maps).
You can take that function and calculate its rms value.
That would be its rms deviation from the average, and you can
convert that to an estimated standard deviation (or simply call it
because of the large number of data points in this function). Sigma
is the standard deviation, and it's a quantitative way of assessing
the noise level of the map.
So you can then ask the following question for any peak in the map:
Is this peak significant or not?
One way to decide on that is to ask how much larger is this peak
than the estimated standard deviation of the map?
High peaks, because they are much above the noise, are more
significant than are the low peaks. And high peaks are those that
will be shown on your graphics screen as you increase the sigma
level of the contours.
===
