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. The Company accepts no liability or responsibility > for any onward transmission or use of emails and attachments > having left the Astex Therapeutics domain. Unless expressly > stated, opinions in this message are those of the individual > sender and not of Astex Therapeutics Ltd. The recipient > should check this email and any attachments for the presence > of computer viruses. Astex Therapeutics Ltd accepts no > liability for damage caused by any virus transmitted by this > email. E-mail is susceptible to data corruption, > interception, unauthorized amendment, and tampering, Astex > Therapeutics Ltd only send and receive e-mails on the basis > that the Company is not liable for any such alteration or any > consequences thereof. > Astex Therapeutics Ltd., Registered in England at 436 > Cambridge Science Park, Cambridge CB4 0QA under number 3751674 >
