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/>
