Thanks, Ian, this is very helpful. Data are 50 - 2.4 A, 90% complete,
70% in 2.5 - 2.4 A shell. Rf/R = 0.235/0.194 (with the few key atoms
omitted; they lie on the 4-fold axis, by the way). <B> = 60 A^2. P4212,
~12,000 atoms in the model. Do these stats impact your recommendations
at all, or raise new potential problems? Dave
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On
> Behalf Of Ian Tickle
> Sent: Thursday, August 21, 2008 8:03 PM
> To: [log in to unmask]
> Subject: Re: [ccp4bb] How best to scale together absolute and
> Fo-Fc density maps?
>
>
> Hi David
>
> One big problem you have here is that, depending on the low & high
> resolution cutoffs and the completeness of your X-ray data, there will
> be Fourier series termination and phase error effects on both the
> electron density maxima and minima. The effects will be to reduce the
> peak heights and broaden the peak widths of your atoms (by an amount
> that is B-factor dependent), and also to introduce both +ve & -ve
> 'ripples', which means that you can't assume that the Fo-Fc map is all
> positive, even if there are no wrongly placed atoms (or atoms with
> errors in occupancy or B factor) in your model. So I think correction
> for the missing F000 term is the least of your worries! That said, I
> would say the answer to your question is to match the map means since
> these depend directly on F000. Matching the map sigmas and/or the
> histograms as you suggest will also take out some of the
> differences due
> to the aforementioned resolution & phase error effects, but
> by no means
> all.
>
> Cheers
>
> -- Ian
>
> > -----Original Message-----
> > From: [log in to unmask]
> > [mailto:[log in to unmask]] On Behalf Of Borhani, David
> > Sent: 21 August 2008 23:20
> > To: [log in to unmask]
> > Subject: How best to scale together absolute and Fo-Fc density maps?
> >
> > I've computed an electron density map, on an absolute scale,
> > from the atomic positions of a molecular dynamics simulation.
> > I would like to compare this map, in particular a few peaks
> > in it, to a (sigmaA-weighted) Fo-Fc map, calculated from a
> > randomly-shaken & refined (with a few key atoms at zero
> > occupancy) x-ray structure. Although I don't know F(000)
> > exactly, I could estimate it, as well as [F(000),obs -
> > F(000),calc], if needed (i.e., I know which atoms are
> > "missing" in the Fo-Fc map, and there are no atoms in the
> > model that need to be removed).
> >
> > Three ways I've considered doing this:
> >
> > 1. Shift the Fo-Fc map values so that it's minimum value
> > becomes zero, then scale it so that it's total electron count
> > equals my (absolute) MD map. I see this as applying
> > [F(000),obs - F(000),calc], followed by (arbitrary) scaling.
> > 2. Match map means and sigmas, and scale them together.
> > 3. Match histograms from each map, applying a linear
> > transformation to get the Fo-Fc map non-negative and its
> > histogram peak position the same as the MD map.
> >
> > Are any of 1 - 3 absurd or stupid? Preferred? A better way
> altogether?
> >
> > Thanks!
> > David Borhani, Ph.D.
> > D. E. Shaw Research, LLC
> > 120 West Forty-Fifth Street, 39th Floor
> > New York, NY 10036
> > [log in to unmask]
> > 212-478-0698
> > http://www.deshawresearch.com <http://www.deshawresearch.com/>
> >
>
>
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