Re: [ccp4bb]: refmac fom

[Bart Hazes <bhazes@ualberta.ca>]

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On Tue, 15 Jan 2002, 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 ;-).
>
> 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) ?

As you already list above, FWT and PHWT are for the weighted "2Fo-Fc" map
(2mFo-DFcalc). So m and it's buddy D are already included. The FOM is also
given separately in cases where you want to use PHIC for other purposes as
mentioned by Eleanor.


> 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?

Eleanor already indicated that the refmac map used D*Fc terms for Rfree
reflections. This will make the purists happy, but I wonder if it is the best
thing to do. Really, how big is the risk of introducing model bias by a clumsy
human trying to best fit a piece of model into the density. We are not talking
about clever software adjusting thousands of parameters to "force" a fit
between model and observations. Perhaps lavishly adding waters to any positive
density feature would introduce some bias but I hope us humans aren't THAT
clumsy. The disadvantage of using D*Fc is that it doesn't contain ANY
information about how to modify the current model to resemble the real
structure more closely. It just contributes a weighted down echo of the Fcalc
density. This may make the density a bit more beautiful and give the
suggestion that your model fits the density better than it really does. So
instead of model bias we create mind bias. Just imagine the silly example that
you select 100% of reflections for the Free set leading to the use of D*Fc for
all reflections. The map would probably look very good. My gut feeling is that
the real purists should leave out the Rfree reflections completely and the
practicalists would include them just like the working set reflection. The
D*Fc option seems half-hearthed at best.

In Olympic tradition: Let the flames begin...

Bart

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