PLATON SQUEEZE: a tool for the calculation of the disordered solvent contribution to the calculated structure factors
PLATON SQUEEZE: a tool for the calculation of the disordered solvent contribution to the calculated structure factors
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DOI：
10.1107/s2053229614024929
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发表时间：
2015-01-01
影响因子：
0.8
通讯作者：
Spek, Anthony L.
中科院分区：
文献类型：
--
作者：
Spek, Anthony L.
晶体结构测定的完成常常受到嵌入的严重无序的溶剂分子或离子的存在的阻碍。在晶体结构的最小二乘精化中，它们对计算的结构因子的贡献必须以某种方式包括在内。传统上，人们尝试了原子论的溶剂无序模型。这种方法通常是优选的，但它并不总是导致令人满意的结果，甚至在结构中的沟道充满连续电子密度的情况下甚至是不可能的。本文将挤压方法作为解决溶剂无序问题的另一种方法。它可以方便地与2014版的最小二乘精化程序SHELXL[Sheldrick(2015)]接口。Acta Cryst.C71。以及接受外部提供的对所计算的结构系数的固定贡献的其他改进程序。Platon挤压工具通过对相优化差电子密度图的溶剂可及区域中的电子密度进行反向傅立叶变换来计算溶剂对结构因子的贡献。实际的最小二乘结构精化被委托给例如SHELXL。Platon Squze和SHELXL的当前版本现在解决了较早实施挤压过程时的几个不必要的复杂问题，这些复杂问题是必要的，因为现在被取代的SHELXL97程序的最小二乘精化不允许输入固定的外部提供的对结构系数计算的贡献。不再需要从观察到的强度中临时减去溶剂贡献，以便能够使用SHELXL进行最小二乘细化，因为如果使用ABIN指令，该程序现在接受来自外部文件(.fab文件)的溶剂贡献。此外，许多含有无序溶剂的孪晶结构现在也可以通过挤压处理。压缩计算的详细信息现在自动包括在CIF存档文件中，以及未合并的反射数据。描述了挤压过程的当前实现，并用三个例子进行了讨论和说明。其中两个基于已发布结构的反射数据，另一个基于为已发布结构生成的合成反射数据。
The completion of a crystal structure determination is often hampered by the presence of embedded solvent molecules or ions that are seriously disordered. Their contribution to the calculated structure factors in the least-squares refinement of a crystal structure has to be included in some way. Traditionally, an atomistic solvent disorder model is attempted. Such an approach is generally to be preferred, but it does not always lead to a satisfactory result and may even be impossible in cases where channels in the structure are filled with continuous electron density. This paper documents the SQUEEZE method as an alternative means of addressing the solvent disorder issue. It conveniently interfaces with the 2014 version of the least-squares refinement program SHELXL [Sheldrick (2015). Acta Cryst. C71. In the press] and other refinement programs that accept externally provided fixed contributions to the calculated structure factors. The PLATON SQUEEZE tool calculates the solvent contribution to the structure factors by back-Fourier transformation of the electron density found in the solvent-accessible region of a phase-optimized difference electron-density map. The actual least-squares structure refinement is delegated to, for example, SHELXL. The current versions of PLATON SQUEEZE and SHELXL now address several of the unnecessary complications with the earlier implementation of the SQUEEZE procedure that were a necessity because least-squares refinement with the now superseded SHELXL97 program did not allow for the input of fixed externally provided contributions to the structure-factor calculation. It is no longer necessary to subtract the solvent contribution temporarily from the observed intensities to be able to use SHELXL for the least-squares refinement, since that program now accepts the solvent contribution from an external file (.fab file) if the ABIN instruction is used. In addition, many twinned structures containing disordered solvents are now also treatable by SQUEEZE. The details of a SQUEEZE calculation are now automatically included in the CIF archive file, along with the unmerged reflection data. The current implementation of the SQUEEZE procedure is described, and discussed and illustrated with three examples. Two of them are based on the reflection data of published structures and one on synthetic reflection data generated for a published structure.