Re: [ccp4bb]: Notation used in ARP_WARP

["S. Ravichandran" <ravi@cmb2.saha.ernet.in>]

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On Fri, 14 Apr 2000, Perkins Lorna wrote:

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> 
> I am currently trying to use ARP_WARP for the first time and I have a query
> which someone may be able to help me with.
> The runnable example within the documentation created by Martin Winn uses
> titles for the maps named 2mFo-DFc and mFo-DFc. Does the m and D within
> these titles actually have any meaning or is this just the correct notation
> for these maps?
> Thanks in advance for any help with this problem
> 
> Lorna Perikns


Hello,

The maps calculated using the coefficients 'm' and 'D' are otherwise
called as SigmaA -weighted map (for full details.. see Read (1996). Acta
Cryst. A42 142-149). 

In short,

m is a Figure of merit, D is equivalent to SigmaA (after correction for
normalisation).

Normal maps have no weightage. viz. 2Fo-Fc or Fo-Fc and so there is a
'unit' scaling coefficients. But in SigmaA weighted maps 'm' and 'D'
(scale it to a factor <1.0) reflects the error and incompleteness of the
model. It is derived from the fit of Iobs to Icalc, and to avoid bias, the
refinement programs like REFMAC (see Murshudov, Vaguine and Dodson (1997)
Acta Cryst D..) deduces it from the Free reflections only.

Hope the experts can write more on this.

Cheers,
Ravi.

======================================================================
|                S.Ravichandran (Graduate student)                   |
|            Crystallography & Molecular Biology Division            |
|                 Saha Institute of Nuclear Physics                  |
|            I/AF, Bidhan Nagar, Calcutta 700 064, INDIA             |
|e-mail:- ravi@cmb2.saha.ernet.in        FAX:-   (91)(033)-337-4637  |
|            URL:-  http://www-bsg.saha.ernet.in/ravi.html           |
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