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: CCP4BB@JISCMAIL.AC.UK > 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
