Re: [ccp4bb]: refmac fom

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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Bernhard Rupp wrote:
> 
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> Dear All :
> 
> Some rtfrm (r for refmac) yields
> FWT and PHWT are amplitude and phase for weighted "2Fo-Fc" map (2mFo-DFcalc)
> 
> Sofar so good. Nice map. Not as nice as Shake&wARP, but it takes about
> a factor of 10**2 less time ;-).
> 

   I guess you mean by  Shake&wARP the map you get after many cycles of
refinement and rebuilding? It should be better, but of course much more
calculation has gone into generating it..

> more rtfrm:
> FOM = <m> - The "figure of merit" for this reflection.
> How do/can I use this particular FOM in a map?
> FP*FOM PHIC is quite a biased map. Where did m's buddy D go?
> Rtfp (paper) ?


 Well - I only use it if I want to use the PHIC for some other purpose
than rebuilding - for instance you hope now you can find your anomalous
scatterers as markers for the building..
 You would do a map DANO, PHIC , FOM.

Or if you had a putative derivative : You could look at the difference
map;
Fph-Fp, PHIC, FOM.

Otherwise I dont think it is very useful. 
Guy likes to look at Fo FOm PHIC maps - and sometimes at lower
resolutions they are better - estimating D at 3A from incomplete data
can be tricky!
 > 
> Also (Brent as well raised the question), qtfm (q for quoting):
> 
> "Rebuilding into these 2mFo-DFcalc and mFo-DFcalc maps
> seems to be easier than using classic nFO-(n-1)FC and difference maps,
> consistent with the established technique for SigmaA style maps.
> One advantage here is that since the m and D values are based on the Free
> set
> of reflections they are less biased than the values obtained by the CCP4
> version of SIGMAA after refinement"
> 
> Ok I can see that for the first (no previous rebuild) map - but then
> in further cycles, haven't you actually taken info from your
> crossvalidation set and (real space) refined against it?


 The 2mFo-DFc coefficients do not include the Free R reflections; those
terms are set = D*Fc, so there should not be corruption of the
crossvalidation set..

 That IS in the paper - maybe not in the fm..


 But if you insist on using nFO-(n-1)FC maps, yes; the cross validation
set will be corrupted, although there is an option in FFT to exclude
them, not that I think many people use it!

 Eleanor

> 
> Best, BR
> 
> -----------------------------------------------------------------
> Bernhard Rupp
> Macromolecular Crystallography and Structural Genomics
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