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首页> 外文期刊>Acta crystallographica. Section D, Structural biology >Direct calculation of cryo-EM and crystallographic model maps for real-space refinement
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Direct calculation of cryo-EM and crystallographic model maps for real-space refinement

机译：直接计算冷冻电镜和晶体学模型图，实现实时空间细化

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摘要

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 limited-resolution 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.
机译：这项工作地址计算的问题从一个原子模型的极限分辨率的地图在低温电子显微镜和x射线中子结晶学,包括情况解决不同的分子到另一个地方。改进与实验进行比较地图。计算地图不仅要再现实验中包含的结构特点地图还本金地图扭曲。这些模型映射可以获得没有使用傅里叶变换,但类似于密度分布,作为一个个体原子笔的贡献。原子密度图像,是原子密度演变反映的扭曲实验地图,特别是的损失决议。由一个中央峰傅里叶包围涟漪。图片应该削减一些距离。表明,达到一个合理的准确性等距离应该明显大于通常应用在计算距离密度分布。速度缓慢的振幅傅里叶波纹减少。意味着至少有一些涟漪包括在计算为了获得一张地图这是足够精确的。功能描述这些原子的贡献靠,对于一个给定的原子类型,分辨率和原子位移参数值。峰值和原子的傅里叶涟漪图像,这些函数的表示的特别设计,集中在一个球壳和不同分析原子参数。工作,力量的依赖生成的映射精度的准确性和原子位移参数截断距离,即波纹的数量包括在原子密度图像,进行了分析。这个分析是完成实际的方面计算的非齐次的地图决议。从一个原子模型作为极限分辨率的地图需要一个大的原子的贡献截断半径扩展超出了中央原子图像的峰值和第一个傅里叶涟漪。这样的计算表示原子的细节原子的贡献,分析功能坐标,原子位移参数和当地的决议。

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