Chodkiewicz Michał L, Migacz Szymon, Rudnicki Witold, Makal Anna, Kalinowski Jarosław A, Moriarty Nigel W, Grosse-Kunstleve Ralf W, Afonine Pavel V, Adams Paul D, Dominiak Paulina Maria
Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ulica Żwirki i Wigury 101, Warszawa, 02-089, Poland.
Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland.
J Appl Crystallogr. 2018 Feb 1;51(Pt 1):193-199. doi: 10.1107/S1600576717015825.
It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called , 'densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed, is an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.
最近已经确定，通过使用一组非球形赝原子而不是传统的原子形状因子球形模型，可以提高晶体结构X射线精修中结构参数的准确性。然而，这是以增加基础计算的复杂性为代价的。为了便于更广泛的晶体学家群体采用这种更先进的电子密度模型，已经开发了一种名为“结构化学和分子生物学中的密度”的新软件实现。它解决了在现代计算架构上提供高性能的挑战。通过针对多核处理器和图形处理单元（使用CUDA）的并行化选项，该库具有计算X射线散射因子及其相对于结构参数的导数的功能，可以访问散射因子计算的中间步骤（从而允许对基础电子密度模型进行修改实验），并提供基本结构晶体学操作的工具。“结构化学和分子生物学中的密度”遵循宽松的（麻省理工学院）许可协议，是一个开源C++库，可以嵌入到用于X射线结构精修的学术和商业工具中。
