The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.
The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA, 92037, USA.
Prog Biophys Mol Biol. 2021 Mar;160:53-65. doi: 10.1016/j.pbiomolbio.2020.06.003. Epub 2020 Jul 6.
A complete understanding of how an orientation distribution contributes to a cryo-EM reconstruction remains lacking. It is necessary to begin critically assessing the set of views to gain an understanding of its effect on experimental reconstructions. Toward that end, we recently suggested that the type of orientation distribution may alter resolution measures in a systematic manner. We introduced the sampling compensation factor (SCF), which incorporates how the collection geometry might change the spectral signal-to-noise ratio (SSNR), irrespective of the other experimental aspects. We show here that knowledge of the sampling restricted to spherical surfaces of sufficiently large radii in Fourier space is equivalent to knowledge of the set of projection views. Moreover, the SCF geometrical factor may be calculated from one such surface. To aid cryo-EM practitioners, we developed a graphical user interface (GUI) tool that evaluates experimental orientation distributions. The GUI returns plots of projection directions, sampling constrained to the surface of a sphere, the SCF value, the fraction of the empty region of Fourier space, and a histogram of the sampling values over the points on a sphere. Finally, a fixed tilt angle may be incorporated to determine how tilting the grid during collection may improve the distribution of views and Fourier space sampling. We advocate this simple conception of sampling and the use of such tools as a complement to the distribution of views to capture the different aspects of the effect of projection directions on cryo-EM reconstructions.
完全理解取向分布如何有助于低温电子显微镜重建仍然缺乏。有必要开始批判性地评估视图集，以了解其对实验重建的影响。为此，我们最近提出，取向分布的类型可能以系统的方式改变分辨率度量。我们引入了采样补偿因子（SCF），它结合了采集几何形状如何改变谱信号噪声比（SSNR），而与其他实验方面无关。我们在这里表明，对傅立叶空间中具有足够大半径的球形表面的采样的了解等同于对投影视图集的了解。此外，SCF 几何因子可以从这样的表面之一计算得出。为了帮助低温电子显微镜从业者，我们开发了一个图形用户界面（GUI）工具，用于评估实验取向分布。GUI 返回投影方向图、受约束于球体表面的采样、SCF 值、傅立叶空间空区的分数以及球体上点的采样值的直方图。最后，可以合并固定倾斜角以确定在采集过程中倾斜网格如何改善视图和傅立叶空间采样的分布。我们主张这种简单的采样概念，并使用此类工具作为视图分布的补充，以捕获投影方向对低温电子显微镜重建影响的不同方面。
