Yes - the RMS for the map is weighted by sin beta
Here is the comment:
C Mean & RMS need to be weighted by sin beta, to allow for distortions
c in Eulerian space.
c On the last section, if beta = 90, the weight is 1/2 because of
c symmetry. Here we only need to test for last section, because
c (a) if last section = 180deg, the weight is zero anyway
c (b) if the last section is not 90 or 180, the rms is not valid anyway
Eleanor
On 09/09/2011 05:42 PM, Ian Tickle wrote:
> 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<[log in to unmask]> 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<[log in to unmask]>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
>>>
>>
>>
>
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