Lu Yishun, Adámek Karel, Stefanic Tihana, Duman Ramona, Wagner Armin, Armour Wesley
Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OxfordOX1 3QG, United Kingdom.
Diamond Light Source Harwell Science & Innovation Campus DidcotOX11 0DE United Kingdom.
J Appl Crystallogr. 2024 Nov 4;57(Pt 6):1984-1995. doi: 10.1107/S1600576724009506. eCollection 2024 Dec 1.
Analytical absorption corrections are employed in scaling diffraction data for highly absorbing samples, such as those used in long-wavelength crystallography, where empirical corrections pose a challenge. is an accelerated software package developed to calculate analytical absorption corrections. It accomplishes this by ray-tracing the paths of diffracted X-rays through a voxelized 3D model of the sample. Due to the computationally intensive nature of ray-tracing, the calculation of analytical absorption corrections for a given sample can be time consuming. Three experimental datasets (insulin at λ = 3.10 Å, thermolysin at λ = 3.53 Å and thaumatin at λ = 4.13 Å) were processed to investigate the effectiveness of the accelerated methods in . These methods demonstrated a maximum reduction in execution time of up to 175× compared with previous methods. As a result, the absorption factor calculation for the insulin dataset can now be completed in less than 10 s. These acceleration methods combine sampling, which evaluates subsets of crystal voxels, with modifications to standard ray-tracing. The bisection method is used to find path lengths, reducing the complexity from () to (log ). The gridding method involves calculating a regular grid of diffraction paths and using interpolation to find an absorption correction for a specific reflection. Additionally, optimized and specifically designed CUDA implementations for NVIDIA GPUs are utilized to enhance performance. Evaluation of these methods using simulated and real datasets demonstrates that systematic sampling of the 3D model provides consistently accurate results with minimal variance across different sampling ratios. The mean difference of absorption factors from the full calculation (without sampling) is at most 2%. Additionally, the anomalous peak heights of sulfur atoms in the Fourier map show a mean difference of only 1% compared with the full calculation. This research refines and accelerates the process of analytical absorption corrections, introducing innovative sampling and computational techniques that significantly enhance efficiency while maintaining accurate results.
对于高吸收性样品（如长波长晶体学中使用的样品）的衍射数据缩放，采用了分析吸收校正，因为经验校正存在挑战。 是一个为计算分析吸收校正而开发的加速软件包。它通过对穿过样品的体素化三维模型的衍射X射线路径进行光线追踪来实现这一点。由于光线追踪的计算量很大，对于给定样品的分析吸收校正计算可能很耗时。处理了三个实验数据集（λ = 3.10 Å的胰岛素、λ = 3.53 Å的嗜热菌蛋白酶和λ = 4.13 Å的奇异果甜蛋白），以研究 中加速方法的有效性。与以前的方法相比，这些方法的执行时间最多减少了175倍。因此，胰岛素数据集的吸收因子计算现在可以在不到10秒内完成。这些加速方法将对晶体体素子集进行评估的采样与对标准光线追踪的修改相结合。二分法用于找到路径长度，将复杂度从()降低到(log )。网格化方法涉及计算衍射路径的规则网格，并使用插值来找到特定反射的吸收校正。此外，还利用了针对NVIDIA GPU的优化和专门设计的CUDA实现来提高性能。使用模拟和真实数据集对这些方法进行评估表明，对三维模型进行系统采样能够提供始终准确的结果，且在不同采样率下的方差最小。与完整计算（无采样）相比，吸收因子的平均差异最多为2%。此外，傅里叶图中硫原子的反常峰高与完整计算相比，平均差异仅为1%。这项研究改进并加速了分析吸收校正过程，引入了创新的采样和计算技术，在保持准确结果的同时显著提高了效率。
