Randy, Use of correlation makes normalization superfluous, but as you say it cannot distinguish from the causes of deviation which may not just be missing density.
Pavel, Thanks for the reference. Will look at it more closely. But how is the error being separated into separate error components alpha and beta? Cheers, Hunter On Wed, Feb 22, 2017 at 11:28 AM, Pavel Afonine <[email protected]> wrote: > Hi, > > Is there a straight-forward way to estimate the amount of missing electron >> density that a particular protein structure is missing based on the >> difference between Fo and Fc? >> > > Any refinement or map calculation software that uses likelihood-based > approach does this routinely. In phenix.refine and phenix.maps I coded this > approach : Acta Cryst. (2002). A58, 270-282. Here it calculates alpha/beta > parameters by comparing Fo and Fc taken from free set. alpha is a function > of model error, and beta is proportional to amount of missing scattering. > If you look up the formulas it should be possible to convert alpha into > error in coordinates (in A) and beta into number of missing atoms (of some > general type). ML based estimate of error in model that phenix.refine > reports is actually done this way. > > Pavel > > -- Hunter Moseley, Ph.D. -- Univ. of Kentucky Associate Professor, Dept. of Molec. & Cell. Biochemistry / Markey Cancer Center / Resource Center for Stable Isotope Resolved Metabolomics Not just a scientist, but a fencer as well. My foil is sharp, but my mind sharper still. --------------------------------------------------------------- Email: [email protected] (work) [email protected] (personal) Phone: 859-218-2964 (office) 859-218-2965 (lab) 859-257-7715 (fax) Web: http://bioinformatics.cesb.uky.edu/ Address: CC434 Roach Building, 800 Rose Street, Lexington, KY 40536-0093
