Ah, there's the rub. No, my simple-minded approach was to calc. the MD density, averaged over, e.g. 100,000 MD snapshots (~1 us of time), by placing (5) Gaussians at each instantaneous atomic position, then adding them all up. Each atom got it's correct Gaussian, along with a b-factor of 1 A^2, but other than that the MD maps are "perfect".
By the way, the MD simulation is not in a crystal lattice. I suppose I could take my current MD map, stick it into an artifical but appropriate lattice, FT to structure factors, apply some resolution cutoffs, errors, then FT^-1 to a new map. Do you think it's worth it? Dave > -----Original Message----- > From: Ian Tickle [mailto:[EMAIL PROTECTED] > Sent: Friday, August 22, 2008 2:24 PM > To: Borhani, David > Cc: [email protected] > Subject: RE: [ccp4bb] How best to scale together absolute and > Fo-Fc density maps? > > > 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:[EMAIL PROTECTED] > > Sent: 22 August 2008 15:10 > > To: Ian Tickle; [email protected] > > 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:[EMAIL PROTECTED] On > > > Behalf Of Ian Tickle > > > Sent: Thursday, August 21, 2008 8:03 PM > > > To: [email protected] > > > 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: [EMAIL PROTECTED] > > > > [mailto:[EMAIL PROTECTED] On Behalf Of Borhani, David > > > > Sent: 21 August 2008 23:20 > > > > To: [email protected] > > > > 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 > > > > [EMAIL PROTECTED] > > > > 212-478-0698 > > > > http://www.deshawresearch.com <http://www.deshawresearch.com/> > > > > > > > > > > > > > Disclaimer > > > This communication is confidential and may contain privileged > > > information intended solely for the named addressee(s). It > > > may not be used or disclosed except for the purpose for which > > > it has been sent. If you are not the intended recipient you > > > must not review, use, disclose, copy, distribute or take any > > > action in reliance upon it. If you have received this > > > communication in error, please notify Astex Therapeutics Ltd > > > by emailing [EMAIL PROTECTED] and destroy all > > > copies of the message and any attached documents. > > > Astex Therapeutics Ltd monitors, controls and protects all > > > its messaging traffic in compliance with its corporate email > > > policy. 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