Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.
Acta Crystallogr D Struct Biol. 2023 Sep 1;79(Pt 9):796-805. doi: 10.1107/S2059798323005776. Epub 2023 Aug 16.
X-ray diffraction enables the routine determination of the atomic structure of materials. Key to its success are data-processing algorithms that allow experimenters to determine the electron density of a sample from its diffraction pattern. Scaling, the estimation and correction of systematic errors in diffraction intensities, is an essential step in this process. These errors arise from sample heterogeneity, radiation damage, instrument limitations and other aspects of the experiment. New X-ray sources and sample-delivery methods, along with new experiments focused on changes in structure as a function of perturbations, have led to new demands on scaling algorithms. Classically, scaling algorithms use least-squares optimization to fit a model of common error sources to the observed diffraction intensities to force these intensities onto the same empirical scale. Recently, an alternative approach has been demonstrated which uses a Bayesian optimization method, variational inference, to simultaneously infer merged data along with corrections, or scale factors, for the systematic errors. Owing to its flexibility, this approach proves to be advantageous in certain scenarios. This perspective briefly reviews the history of scaling algorithms and contrasts them with variational inference. Finally, appropriate use cases are identified for the first such algorithm, Careless, guidance is offered on its use and some speculations are made about future variational scaling methods.
X 射线衍射使得常规确定材料的原子结构成为可能。其成功的关键是数据处理算法,该算法允许实验人员从衍射图案中确定样品的电子密度。定标是这个过程中的一个基本步骤,它用于估计和校正衍射强度中的系统误差。这些误差来自样品不均匀性、辐射损伤、仪器限制以及实验的其他方面。新的 X 射线源和样品输送方法,以及新的关注结构随扰动变化的实验,对定标算法提出了新的要求。传统上,定标算法使用最小二乘优化来拟合常见误差源的模型,以将观察到的衍射强度拟合到相同的经验标度上。最近,已经证明了一种替代方法,该方法使用贝叶斯优化方法,即变分推理,同时推断合并数据以及系统误差的校正或比例因子。由于其灵活性,这种方法在某些情况下证明是有利的。本文简要回顾了定标算法的历史,并将其与变分推理进行了对比。最后,为第一个这样的算法 Careless 确定了合适的用例,并提供了关于其使用的指导,并对未来的变分定标方法进行了一些推测。