Re: [ccp4bb]: Solomon with molecular replacement Phases

[Jay Pandit <pandit@pfizer.com>]

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Steven Herron wrote:
> > 
>  Dear CCP4'ers,
> 
>      I have been hearing great things about Solomon and I would like to
> try it, but my phase information is derived from molecular replacement.
> The documentation for Solomon implies that MIR or MAD phase information
> is needed.
>     Is there a way I can use Solomon with molecular replacement or is
> there a similar program which can handle my phase information?
> 

 I hope that we get some kind of a definitive answer to this question,
which keeps popping up in different forms on this bb. ( Eleanor?, Kevin
? )
  Density modification programs like Solomon work on phase probability
distributions, which typically come from experimental phase
determination (MIR, MAD , SIR ). They succeed in "improving" these
phases, because they add information derived from the molecular envelope
back to the phase probability distributions. The results are often
spectacular.
 Molecular replacement phases are unimodal - by definition, they are
calculated from a model, so there is no scope for "improving" them. One
could weight them proportionately to (Fo-Fc) , or more rigorously, with
SigmaA weights. These weights could then be converted into a unimodal
"probability distribution", and fed into solomon or dm, which would then
sharpen it based on the molecular envelope. I believe that people do
this, and I am interested in learning if it really works, and why. It is
not clear to me why this would give a better map than a SigmaA weighted,
bulk-solvent corrected 2mFo-DFc map with Fc's from your MR solution.
Of course, if you have NCS, then significant improvement can be had by
averaging, as long as you can define your operators precisely. Solomon
and dm incorporate averaging in the general density modification
procedure, and can be used for phase improvement.
Cheers,
Jay

-- 
 Jay Pandit
 Pfizer Central Research                        Phone:  (1) 860 441 3738
 Eastern Point Road                             Fax  :  (1) 860 441 4734
 Groton CT 06340 , USA                          email: pandit@pfizer.com