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.
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg06969.html http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg15273.html 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 -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
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