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Re: [ccp4bb]: Solomon with molecular replacement Phases

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Our experience is that density modification does give some useful
improvements in MR when the molecular replacement is substantially incomplete
(e.g. protein model used to phase protein-DNA complex) and especially when
you can mask out the volume in which the 'missing' parts of the structure are
expected to appear, so that they are not flattened to solvent density.

Laurence Pearl

Jay Pandit wrote:

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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


  Laurence H. Pearl

  Section of Structural Biology, Institute of Cancer Research
  Chester Beatty Laboratories,  237 Fulham Road
  London SW3 6JB, UK

  Phone +44-207-970 6045 : Secretary +44-207-970 6046
  FAX   +44-207-970 6051 : E-Mail l.pearl@icr.ac.uk
  " Live Simply and do Serious Things .. " - Dorothy Crowfoot Hodgkin