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RE: [ccp4bb]: Solomon with molecular replacement Phases
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We have had first hand experience with the "spectacular" results from
Solomon and would be interested to know if similar results are possible from
MR phases. I have considered trying some procedures to smear the MR phic's
and truncate the resolution then sigmaa weighting for pseudo FOMS followed
by solvent flipping phase extension. In lieu of this though, you might try
wARP straight away if you have sufficient resolution. We have also seen
"spectacular" results from wARP.
If it crystallizes, it's important...
Brent W. Segelke, Ph.D.
Lawrence Livermore National Laboratory
POB 808 L452
Livermore CA 94551
(925) 424-3130 (FAX)
> -----Original Message-----
> From: firstname.lastname@example.org [mailto:email@example.com]On Behalf Of
> Jay Pandit
> Sent: Tuesday, February 29, 2000 1:40 PM
> To: Steven Herron
> Cc: CCP4 News Group
> Subject: Re: [ccp4bb]: Solomon with molecular replacement Phases
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> *** CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html ***
> 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
> 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.
> Jay Pandit
> Pfizer Central Research Phone: (1) 860 441 3738
> Eastern Point Road Fax : (1) 860 441 4734
> Groton CT 06340 , USA email: firstname.lastname@example.org