Re: [ccp4bb]: ccp4bb: Can a correct partial model degrade experimental phases?

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

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wgscott@chemistry.ucsc.edu wrote:
> 
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> Hi folks:
> 
> I was just asked if a correct partial model might degenerate the
> quality of phases when performing partial model phase combination,
> using sigma-a weighting.
> 
> Say I have an MIR or MAD phase set and build only 5 to 10% of the atoms
> into electron density.  Let's further assume that the model is simply
> incomplete, not
> incorrect (in the sense of wrongly-placed atoms).
> 
> My initial answer was that it could only help or do nothing, but was
> then asked if omitting atoms from the molecule is the equivalent of
> having an "incorrect" model in the sense that most of the scattering
> atoms are being modeled in as nothing (or solvent).  Would a partial
> model having only 5 or 10% of the atoms therefore degrade the phases?
> If so, at what point would you break even?
> 
> Bill Scott


 Theoretically it should help - any correct phase information is good..
However this pre=supposes that you can weight the two sources of
information properly and that is not always easy..
 Ths phase comtribution from the 10% model is pretty weak, and in most
cases you would expect that the MIR info should dominate. However it can
help - for example SHARP uses the model phase from the sub-structure to
get phase estimates for centric data from a SAD experiment, where there
is no exptl info for those reflections. And the experts say this helps.
It is very hard to quantify - obv. there are other phase improvements
going on at the same time..
  Eleanor
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Eleanor J.Dodson, York Structural Biology Laboratory,
                  Chemistry Department, 
                  University of York, Y01 5DD Heslington, U.K.
Tel: Work: +44 (1904) 32 82 53  Home +44 (1904) 42 44 49
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