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Dear P K, Is it just me or are other people also enjoying the 'name guessing game' regarding posts to ccp4bb? This one came from P K <[log in to unmask]> I could think of a few people with the initials 'P K' - not sure if everyone is a great biologist (as opposed to just a plain good one). Wouldn't it be good manner to show your name on posts to the ccp4bb? There is no need for shoe size or bank account, but otherwise this turns into a big anonymous mailing list (and this is not quite fair to all the helpful people making their name visible - at the danger of geting quoted 5 years later or some future employer or funding agency checking on their past record). Cheers Clemens On Wed, Jul 30, 2008 at 01:58:26PM +0200, 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. > === -- *************************************************************** * 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) ***************************************************************