高分辨率噪声替代法测量单颗粒电子冷冻显微镜三维结构测定中的过拟合和分辨率验证。
High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy.
机构信息
MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K.
出版信息
Ultramicroscopy. 2013 Dec;135:24-35. doi: 10.1016/j.ultramic.2013.06.004. Epub 2013 Jun 21.
Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an unbiased FSC from the two curves, even when a substantial amount of overfitting is present. The approach is software independent. The user is therefore completely free to use any established method or novel combination of methods, provided the HR-noise test is carried out in parallel. Applying this procedure to cryoEM images of beta-galactosidase shows how overfitting varies greatly depending on the procedure, but in the best case shows no overfitting and a resolution of ~6 Å. (382 words).
三维(3D)结构通过单颗粒电子低温显微镜(cryoEM)确定,涉及初始 3D 模型的计算,随后对各个颗粒图像的取向和所得 3D 图进行广泛的迭代改进。由于在高分辨率下图像中的噪声比信号多得多,这就有可能在 3D 图中增强噪声,从而对所达到的分辨率产生错误的印象。在最终的 3D 图中,在其极限分辨率下,信号与噪声之间的平衡取决于图像处理过程,并且不容易预测。cryoEM 社区越来越意识到如何避免这种过度拟合和分辨率的高估。同样,人们不愿意使用两种主要的避免方法,因为它们给出的分辨率估计较低,有些人认为这过于悲观。在这里,我们描述了一种简单的测试方法,该方法与任何图像处理协议兼容。该测试可用于测量最终 3D 图中存在的过度拟合的信号量和噪声量。我们已经将该方法应用于使用几种图像处理软件包的酶β-半乳糖苷酶的两组不同的 cryoEM 图像。我们的程序涉及用所选分辨率以外的初始粒子图像堆栈的傅立叶分量替换要么来自相邻背景区域的傅立叶分量,要么替换为粒子结构因子的相位的简单随机化。这种替代噪声因此具有与原始数据相同的光谱功率分布。用实验数据获得的 3D 图的傅立叶壳相关(FSC)图与用高分辨率噪声(HR-noise)替代的相同数据的 FSC 图进行比较,可以明确测量过度拟合的程度,并进行分辨率评估。即使存在大量过度拟合,也可以使用简单的公式从两条曲线计算无偏 FSC。该方法是独立于软件的。因此,用户完全可以自由使用任何已建立的方法或新颖的方法组合,只要并行进行 HR-noise 测试即可。将该程序应用于β-半乳糖苷酶的 cryoEM 图像表明,过度拟合的程度随程序而有很大差异,但在最佳情况下没有过度拟合,分辨率约为 6 Å。