审稿意见-原子位置解析方法填写

DJ_Tokyo

相关软件或概念：Olex2[1] (Version: Olex2-1.5); PLATON[2] (Version: 60124); SHELXL[3] (Version: SHELXL-2019/3)

审稿意见

A coupleof fields seem blank after re-refinements: "_atom_sites_solution_hydrogens","_atom_sites_solution_primary ?", "_atom_sites_solution_secondary?", please add for completeness.

该审稿意见是让把CIF[4]中三个条目“_atom_sites_solution_hydrogens”“_atom_sites_solution_primary”和“_atom_sites_solution_secondary”的项目值填上。

查阅CIF词典（https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/index.html），找到“_atom_sites_solution_primary”“_atom_sites_solution_secondary”和“_atom_sites_solution_hydrogens”，其定义如下：

Core  dictionary (coreCIF) version 2.4.5		核心词典（coreCIF）版本2.4.5
_atom_sites_solution_primary    _atom_sites_solution_secondary    _atom_sites_solution_hydrogens		_atom_sites_solution_primary    _atom_sites_solution_secondary    _atom_sites_solution_hydrogens
Name:		名称：
'_atom_sites_solution_primary'    '_atom_sites_solution_secondary'    '_atom_sites_solution_hydrogens'		'_atom_sites_solution_primary'    '_atom_sites_solution_secondary'    '_atom_sites_solution_hydrogens'
Definition:		定义：
Codes  which identify the methods used to locate the initial atom sites. The  *_primary code identifies how the first atom sites were determined; the  *_secondary code identifies how the remaining non-hydrogen sites were  located; and the *_hydrogens code identifies how the hydrogen sites were  located.		识别用于定位初始原子位点的方法的代码。*_primary代码标识第一个原子位点是如何确定的；*_secondary代码标识剩余的非氢位点是如何定位的；以及*_hydrogens代码标识氢位点是如何定位的。
Ref:  Sheldrick, G. M., Hauptman, H. A., Weeks, C. M., Miller, R. and Us\'on, I.  (2001). Ab initio phasing. In International Tables for Crystallography, Vol.  F. Crystallography of biological macromolecules, edited by M. G. Rossmann and  E. Arnold, ch. 16.1. Dordrecht: Kluwer Academic Publishers.		参考文献：Sheldrick,  G. M., Hauptman, H. A., Weeks, C. M., Miller, R. and Us\'on, I. (2001). Ab  initio phasing. In International Tables for Crystallography, Vol. F.  Crystallography of biological macromolecules, edited by M. G. Rossmann and E.  Arnold, ch. 16.1. Dordrecht: Kluwer Academic Publishers.
The  data value must be one of the following:		数据值必须是以下值之一：
difmap	difference  Fourier map		差值傅里叶图
vecmap	real-space  vector search		实空间矢量搜索
heavy	heavy-atom  method		重原子法
direct	structure-invariant  direct methods		结构不变直接法
geom	inferred  from neighbouring sites		由相邻位点推断
disper	anomalous-dispersion  techniques		反常散射技术
isomor	isomorphous  structure methods		同构结构法
notdet	coordinates  were not determined		坐标未确定
dual	dual-space  method (Sheldrick et al., 2001)		双空间法(Sheldrick  et al., 2001)
iterative	iterative  algorithm, e.g. charge flipping [Oszl\'anyi, G. and S\"uto, A. (2004).  Acta Cryst. A60, 134-141]		迭代算法，例如电荷翻转[Oszl\'anyi,  G. and S\"uto, A. (2004). Acta Cryst. A60, 134-141]
other	a  method not included elsewhere in this list		此列表中其他位置未包含的方法

如果用SHELXT[5]程序的Intrinsic Phasing（或XM[3b]或SHELXD[6]的Dual Space）解析结构，“_atom_sites_solution_primary”则为“dual”，氢原子采用理论加氢，则“_atom_sites_solution_hydrogens”为“geom”，其他非氢原子通过傅里叶合成（即通过残余电子密度峰（Q峰）确定），则“_atom_sites_solution_secondary”为“difmap”。

如果用SHELXS[7]程序的直接法（Direct Methods[8]）解析结构，则“_atom_sites_solution_primary”则为“direct”。

如果用SHELXS[7]程序的重原子法（Patterson Method[9]）或结构扩展法（Structure Expansion）解析结构，则“_atom_sites_solution_primary”则为“heavy”。

如果用Superflip[10]程序或者olex2.solve程序的电荷翻转法（Charge Flipping[11]）解析结构，则“_atom_sites_solution_primary”则为“iterative”。

如果结构中氢原子既有理论加氢确定的，又有通过Q峰确定的，则“_atom_sites_solution_hydrogens”为“mixed”。

如果结构中不含氢原子，则“_atom_sites_solution_hydrogens”为“.”。

此处仅罗列了部分可能的情况，还有其他的解析程序由于编者未曾使用过，因此未予展示。

总之，解析完成后，应当根据实际情况填写“_atom_sites_solution_primary”“_atom_sites_solution_secondary”和“_atom_sites_solution_hydrogens”。

视频操作演示请参阅：

审稿意见-原子位置解析方法填写：https://www.bilibili.com/video/BV11B421k74k

参考文献

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[3](a) Sheldrick, G. M. SHELXL-2019/2, Program for Crystal Structure Refinement,University of Göttingen, Germany, 2019. (b) Sheldrick, G. M. A short history ofSHELX. Acta Cryst. 2008, A64, 112–122. (c) Sheldrick, G. M.Crystal structure refinement with SHELXL.Acta Cryst. 2015, C71, 3–8. (d)Lübben, J.; Wandtke, C. M.; Hübschle, C. B.; Ruf, M.; Sheldrick, G. M.;Dittrich, B. Aspherical scattering factors for SHELXL – model, implementation and application. Acta Cryst. 2019, A75, 50–62.

[4](a) Hall, S. R.; Allen, F. H. Brown, I. D. The Crystallographic InformationFile (CIF): a New Standard Archive File for Crystallography. Acta Cryst. 1991, A47, 655–685. (b)Hall, S. R. The STAR File: A New Format for Electronic Data Transfer andArchiving. J. Chem. Inf. Comput. Sci.1991, 31, 326–333. (c) Hall, S. R.; Spadaccini, N. The STAR File:Detailed Specifications. J. Chem. Inf.Comput. Sci. 1994, 34, 505–508.

[5]Sheldrick, G. M. SHELXT – Integratedspace-group and crystal structure determination. Acta Cryst. 2015, A71, 3–8.

[6] Usón, I.; Sheldrick, G. M. An introductionto experimental phasing of macromolecules illustrated by SHELX; new autotracingfeatures. Acta Cryst. 2018, D74, 106–116.

[7]Sheldrick, G. M. SHELXS-97, Program for Crystal Structure Solution.University of Göttingen, Germany, 1997.

[8](a) Sheldrick, G. M. Phase Annealing in SHELX-90:Direct Methods for Larger Structures. ActaCryst. 1990, A46, 467–473. (b)Sheldrick, G. M.; Usón, I. Advances in direct methods for proteincrystallography. Curr. Opin. Struct. Biol. 1999, 9, 643–648. (c) Sheldrick, G. M., Hauptman, H. A., Weeks, C. M.,Miller, R. & Usón, I. InternationalTables for Crystallography, Vol. F, edited by E. Arnold and M. Rossmann,pp. 333 345. Dordrecht: Kluwer Academic Publishers, 2001. (d) Giacovzaao, C. Phasing in Crystallography. Oxford:IUCr/Oxford University Press, 2014.

[9]Patterson, A. L. A Fourier Series Method for the Determination of theComponents of Interatomic Distances in Crystals. Phys. Rev. 1934, 46, 372–376.

[10] Palatinus, L.; Chapuis, G. SUPERFLIP – a computer program for the solution of crystalstructures by charge flipping in arbitrary dimensions. J. Appl. Cryst. 2007, 40, 786-790.

[11] (a) Oszlányi, G.; Sütő, A. Ab initio structure solution by charge flipping. Acta Cryst. 2004, A60, 134–141. (b) Oszlányi,G.; Sütő, A. Ab initio structuresolution by charge flipping. II. Use of weak reflections. Acta Cryst. 2005, A61, 147–152. (c) Oszlányi, G.; Sütő, A.Ab initio neutron crystallography bythe charge flipping method. Acta Cryst.2007, A63, 156–163. (d) Oszlányi, G.; Sütő, A. Czugler, M.; Párkányi, L. ChargeFlipping at Work: A Case of Pseudosymmetry. J.Am. Chem. Soc. 2006, 128, 8392–8393.