Dave

It's hard to say without actually doing the calculations, it may well be
that I'm being too pessimistic about your prospects!  One thing I'm not
clear about is how you actually calculated your map from the MD atomic
positions: did you take into account the resolution limits, data
completeness & B factors (i.e. by going via the Fcalcs for the X-ray
dataset)?  If so then that would clearly eliminate some of the sources
of error, though not of course phase errors due to inadequate modelling
of solvent, anisotropy, anharmonicity, disorder effects etc.

-- Ian

> -----Original Message-----
> From: Borhani, David [mailto:[log in to unmask]] 
> Sent: 22 August 2008 15:10
> To: Ian Tickle; [log in to unmask]
> Subject: RE: [ccp4bb] How best to scale together absolute and 
> Fo-Fc density maps?
> 
> 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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