Rex, sorry, addendum to my last post: the grid points in the Eulerian space of the cross-RF (which is what I assume you're talking about) do not occupy equal volumes in angular space as they would do in a Euclidean space (e.g. a normal electron density map). For example the volume of any grid point on the beta=0 & 180 sections is zero (these sections actually each consist of a line of points, and a line of course occupies no volume). Therefore it's necessary to weight the values in both the mean and the RMSD by the volume of each grid point (= sin(beta)). Whether ALMN actually does this or not would require an examination of the source code, though it's probably quicker to ask Eleanor!
Cheers -- Ian On Fri, Sep 9, 2011 at 5:26 PM, Ian Tickle <ianj...@gmail.com> wrote: > > Hi Rex > > I would assume it's the RMS deviation of the rotation function value from > the mean. If so then it's defined in the same way as the "population > standard deviation" as given here: > http://en.wikipedia.org/wiki/Standard_deviation > > Cheers > > -- Ian > > > On Fri, Sep 9, 2011 at 4:20 PM, REX PALMER <rex.pal...@btinternet.com>wrote: > >> Dear CCP4'ers >> >> In the input instructions for ALMN it says: >> FIND peak maxpek [RMS] [OUTPUT filename] >> Read peak threshold and maximum number of peaks. MAXPEK is the maximum >> number of peaks to find (default = 20). Up to MAXPEK peaks above PEAK will >> be found, and all symmetry related peaks generated. >> If the keyword RMS is present, then the peak threshold is PEAK * RMS >> density, otherwise PEAK is the absolute threshold in the scaled map. >> Question: RMS density of what and what is the formula used? >> >> Rex Palmer >> http://www.bbk.ac.uk/biology/our-staff/emeritus-staff >> http://rexpalmer2010.homestead.com >> > >
