WikiSysop: Created page with "== Citation == Urzhumtsev, Alexandre G. / Urzhumtseva, Ludmila M. / Lunin, Vladimir Y. Direct calculation of cryo-EM and crystallographic model maps for real-space refinement..."

2023-06-28T09:02:23Z

Created page with "== Citation == Urzhumtsev, Alexandre G. / Urzhumtseva, Ludmila M. / Lunin, Vladimir Y. Direct calculation of cryo-EM and crystallographic model maps for real-space refinement..."

New page

== Citation ==

Urzhumtsev, Alexandre G. / Urzhumtseva, Ludmila M. / Lunin, Vladimir Y. Direct calculation of cryo-EM and crystallographic model maps for real-space refinement. 2022. Acta Crystallographica Section D: Structural Biology, Vol. 78, No. 12, 1451-1468

== Abstract ==

This work addresses the problem of the calculation of limited-resolution maps
from an atomic model in cryo-electron microscopy and in X-ray and neutron
crystallography, including cases where the resolution varies from one molecular
region to another. Such maps are necessary in real-space refinement for
comparison with the experimental maps. For an appropriate numeric
comparison, the calculated maps should reproduce not only the structural
features contained in the experimental maps but also the principal map
distortions. These model maps can be obtained with no use of Fourier
transforms but, similar to density distributions, as a sum of individual atomic
contributions. Such contributions, referred to as atomic density images, are
atomic densities morphed to reflect distortions of the experimental map, in
particular the loss of resolution. They are described by functions composed of a
central peak surrounded by Fourier ripples. For practical calculations, atomic
images should be cut at some distance. It is shown that to reach a reasonable
accuracy such a distance should be significantly larger than the distance
customarily applied when calculating density distributions. This is a consequence
of the slow rate with which the amplitude of the Fourier ripples
decreases. Such a large distance means that at least a few ripples should be
included in calculations in order to obtain a map that is sufficiently accurate.
Oscillating functions describing these atomic contributions depend, for a given
atomic type, on the resolution and on the atomic displacement parameter values.
To express both the central peak and the Fourier ripples of the atomic images,
these functions are represented by the sums of especially designed terms, each
concentrated in a spherical shell and depending analytically on the atomic
parameters. In this work, the strength of the dependence of the accuracy of
resulting map on the accuracy of the atomic displacement parameters and on the
truncation distance, i.e. the number of ripples included in atomic density images,
is analyzed. This analysis is completed by practical aspects of the calculation of
maps of inhomogeneous resolution. Tests show that the calculation of limitedresolution
maps from an atomic model as a sum of atomic contributions requires
a large truncation radius extending beyond the central peak of an atomic image
and the first Fourier ripples. The article discusses the practical details of such
calculations expressing atomic contributions as analytic functions of the atomic
coordinates, the atomic displacement parameters and the local resolution.

== Keywords ==

== Links ==

https://scripts.iucr.org/cgi-bin/paper?di5059

== Related software ==

== Related methods ==

== Comments ==

2022Urzhumtsev Direct - Revision history

WikiSysop: Created page with "== Citation == Urzhumtsev, Alexandre G. / Urzhumtseva, Ludmila M. / Lunin, Vladimir Y. Direct calculation of cryo-EM and crystallographic model maps for real-space refinement..."