晶体结构解析组内培训3(结构解析与精修程序)

DJ_Tokyo

晶体结构解析组内培训3(结构解析与精修程序)

⸢结构解析程序⸥（structure solution program）

常见结构解析程序如下：

解析程序	解析算法	参考文献
shelxt.exe  (SHELX)    xt.exe  (Bruker)	Intrinsic  Phasing（本征定相法）	SHELXT[1]
shelxs.exe  (SHELX)    xs.exe  (Bruker)	Direct  Methods（直接法）	SHELXS[2]; Direct Methods[3]; Patterson Method[4]
	Patterson  Method（重原子法）
	Structure  Expansion（结构扩展法）
shelxd.exe  (SHELX)    xm.exe  (Bruker)	Dual Space（双空间法）	SHELXD[5]
superflip.exe	Charge  Flipping（正负交替反转法）	Superflip[6]; Olex2[7];  Charge Flipping[8]
olex2.solve  (Olex2)
sir2019.exe	Standard  Direct Methods（SDM，标准直接法）    Modern  Direct Methods（MDM，现代直接法）    Vive la  Différence（VLD）    Automatic  Patterson Deconvolution（APD）	SIR2019[9]; SDM[10]; MDM[11]; VLD[12];  APD[13]

⸢结构精修程序⸥（structure refinement program）

常见结构精修程序如下：

精修程序	精修方法	参考文献
shelxl.exe  (SHELX)    xl.exe  (Bruker)	Least-Square（最小二乘法）    Conjugate  Gradient Least-Square（共轭梯度最小二乘法）	SHELXL[14]
olex2.refine  (Olex2)	G-N（Gauss-Newton，全矩阵最小二乘法）    L-M（Levenberg-Marquardt，区块精修法）	Olex2[7]

Olex2官网（https://www.olexsys.org/）对这些解析和精修程序有简单的介绍，亦可参阅笔者整理的推文：晶体结构解析和精修程序简介。

⸢图形用户界面⸥（GUI, Graphical User Interface）

常见GUI如下：

GUI	来源	参考文献
Shelxtl	SHEX程序包商业化孪生版本（Bruker AXS销售）	Shelxtl[15]
XShell	Shelxtl中XSHELL独立窗口（Bruker AXS销售）	XShell[16]
ShelXle	德国哥廷根大学Hübschle, C. B.开发	ShelXle[17]
Olex2	英国杜伦大学Dolomanov,  O. V.开发	Olex2[7]
Oscail	爱尔兰国立大学McArdle, P.开发	Oscail[18]
WinGX	英国格拉斯哥大学Farrugia, L.  J.开发	WinGX[19]
X-Seed	密苏里大学哥伦比亚分校Barbour, L.  J.开发	X-Seed[20]

⸢其他程序⸥

程序	来源	参考文献
platon.exe	荷兰乌得勒支大学Spek A. L.开发	PLATON[21]
pwt.exe	PLATON的Windows任务栏	PWT[22]
xprep.exe	Shelxtl的子程序（Bruker AXS销售）	XPREP[23]
xp.exe	Shelxtl的子程序（Bruker AXS销售）	XP[24]
xcif.exe	Shelxtl的子程序（Bruker AXS销售）	XCIF[25]
FinalCif.exe	Kratzerts,  D.开发	FinalCif[26]
encifer.exe	CCDC开发	enCIFer[27]
publcif.exe	Westrip, S. P.开发	publCIF[28]

以下是一些程序下载地址：

SHELX：http://shelx.uni-goettingen.de/

Superflip：http://superflip.fzu.cz/

Olex2：https://www.olexsys.org/

Sir2019：https://www.ic.cnr.it/

ShelXle：https://www.shelxle.org/shelx/eingabe.php

Oscail：https://www.universityofgalway.ie/crystallography/oscailsoftware/

WinGX：https://www.chem.gla.ac.uk/~louis/software/wingx/

PLATON：http://www.chem.gla.ac.uk/~louis/software/platon/

PWT：http://www.chem.gla.ac.uk/~louis/software/platon/

FinalCif：https://dkratzert.de/

enCIFer：https://www.ccdc.cam.ac.uk/

publCIF：https://journals.iucr.org/services/cif/publcif/

[1] Sheldrick,G. M. SHELXT – Integrated Space-Groupand Crystal Structure Determination. ActaCryst. 2015, A71, 3–8. DOI: 10.1107/S2053273314026370.

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

[3](a) Sheldrick, G. M. Phase Annealing in SHELX-90: Direct Methods for LargerStructures. Acta Cryst. 1990, A46, 467–473. DOI:10.1107/S0108767390000277. (b)Usón, I.; Sheldrick, G. M. Advances in direct methods for proteincrystallography. Curr. Opin. Struct. Biol. 1999, 9, 643–648. DOI:10.1016/S0959-440X(99)00020-2. (c)Sheldrick, G. M., Hauptman, H. A., Weeks, C. M., Miller, R. & Usón, I. International Tables for Crystallography,Vol. F, edited by E. Arnold and M. Rossmann, pp. 333–345. Dordrecht: KluwerAcademic Publishers, 2001. (d)Giacovazzo. C. International Tables forCrystallography (2008). Vol. B,ch. 2.2, pp. 215–243. (e)Giacovzaao, C. Phasing in Crystallography.Oxford: IUCr/Oxford University Press, 2014.

[4] PattersonMethod: Patterson,A. L. A Fourier Series Method for the Determination of the Components ofInteratomic Distances in Crystals. Phys.Rev. 1934, 46, 372–376. DOI: 10.1103/PhysRev.46.372.

[5] (a) Usón, I.;Sheldrick, G. M. Advances in Direct Methods for Protein Crystallography. Curr. Opin. Struct. Biol. 1999, 9, 643–648. DOI: 10.1016/S0959-440X(99)00020-2. (b) Sheldrick, G. M.,Hauptman, H. A., Weeks, C. M., Miller, R. & Usón, I. International Tables for Crystallography, Vol. F, edited by E.Arnold and M. Rossmann, pp. 333–345. (c) Sheldrick,G. M. A short history of SHELX. Acta Cryst. 2008, A64, 112–122. DOI: 10.1107/S0108767307043930. (d)Usón,I.; Sheldrick, G. M. An Introduction to Experimental Phasing of MacromoleculesIllustrated by SHELX; New AutotracingFeatures. Acta Cryst. 2018, D74, 106–116. DOI: 10.1107/S2059798317015121.

[6] Palatinus L.;Chapuis G. SUPERFLIP - A ComputerProgram for the Solution of Crystal Structures by Charge Flipping in ArbitraryDimensions. J. Appl. Cryst. 2007, 40, 786–790. DOI: 10.1107/S0021889807029238.

[7] Dolomanov,O. V.; Bourhis, L. J.; Gildea, R. J.; Howard, J. A. K.; Puschmann, H. OLEX2: A Complete Structure Solution,Refinement and **ysis Program. J. Appl. Cryst. 2009, 42, 339–341. DOI: 10.1107/S0021889808042726.

[8] Original articles about charge flipping: (a) Oszlanyi G.; Suto A. Ab Initio Structure Solution by Charge Flipping.Acta Cryst. 2004, A60, 134–141. DOI: 10.1107/S0108767303027569. (b)Oszlanyi G.; Suto A. Ab Initio StructureSolution by Charge Flipping. II. Use of Weak Reflections. Acta Cryst. 2005, A61, 147–152. DOI: 10.1107/S0108767304027746. (c)Oszlányi G.; Süto A. Ab Initio NeutronCrystalography by the Charge Fliping Method. Acta Cryst. 2007, A63, 156–163. DOI: 10.1107/S0108767306055991. (d)Charge flipping in superspace: Palatinus L. Ab Initio Determination of IncommensuratelyModulated Structures by Charge Flipping in Superspace. Acta Cryst. 2004, A60, 604–610. DOI: 10.1107/S0108767304022433. (e)Low-density elimination method: Shiono M.;Woolfson M. M. Direct-Space Methods in Phase Extension and Phase Determination.I. Low-Density Elimination. Acta Cryst.1992, A48, 451–456. DOI: 10.1107/S010876739101471X.(f) Chargeflipping on powder diffraction data: Baerlocher Ch.; McCusker L. B.;Palatinus L. Charge Flipping Combined with Histogram Matching to Solve Complex CrystalStructures from Powder Diffraction Data. Z.Kristallogr. 2007, 222, 47–53. DOI: 10.1524/zkri.2007.222.2.47.

[9]Burla, M. C.; Caliandro, R.; Carrozzini, B.; Cascarano, G. L.; Cuocci, C.; Giacovazzo,C.; Mallamo, M.; Mazzone, A.; Polidori, G. Crystal Structure Determination andRefinement via SIR2014. J. Appl. Cryst. 2015, 48, 306–309. DOI: 10.1107/S1600576715001132.

[10] Burla, M. C.; Caliandro, R.; Camalli, M.; Carrozzini,B.; Cascarano, G. L.; De Caro, L.; Giacovazzo, C.; Polidori, G.; Spagna, R. SIR2004: An Improved Tool for Crystal StructureDetermination and Refinement. J. Appl.Cryst. 2005, 38, 381–388. DOI:10.1107/S002188980403225X.

[11] Burla, M. C.; Giacovazzo, C.; Polidori, G. A RobustTangent Procedure. J. Appl. Cryst. 2013, 46, 1592–1602. DOI:10.1107/S0021889813024709.

[12] (a) Burla, M. C.; Caliandro,R.; Giacovazzo, C.; Polidori, G. The Difference Electron Density: AProbabilistic Reformulation. Acta Cryst.2010, A66, 347–361. DOI: 10.1107/S010876731000365X.(b) Burla, M. C.; Carrozzini, B.; Polidori,G. From a Random to the Correct Structure: the VLD Algorithm. J. Appl. Cryst. 2010, 43, 825–836. DOI: 10.1107/S0021889810018285. (c) Burla,M. C.; Carrozzini, B.; Cascarano, G. L.; Giacovazzo, C.; Polidori, G. Advancesin the VLD Algorithm. J. Appl. Cryst.2011, 44, 1143–1151. DOI:10.1107/S0021889811042154. (d) Burla, M. C.; Giacovazzo,C.; Polidori, G. Phasing Medium-Size Structures and Proteins by the VLDAlgorithm. J. Appl. Cryst. 2011, 44, 193–199. DOI:10.1107/S002188981005394X.

[13] (a) Burla, M. C.;Caliandro, R.; Carrozzini, B.; Cascarano, G. L.; De Caro, L.; Giacovazzo, C.; Polidori,G. Siliqi, D. The Revenge ofthe Patterson Methods. I. Protein AbInitio Phasing. J. Appl. Cryst. 2006, 39, 527–535. DOI: 10.1107/S0021889806017894.(b) Burla, M. C.;Caliandro, R.; Carrozzini, B.; Cascarano, G. L.; De Caro, L.; Giacovazzo, C.; Polidori,G. Siliqi, D. Use of Patterson-BasedMethods Automatically to Determine the Structures of Heavy-Atom-Containing Proteinswith up to 6000 Non-Hydrogen Atoms in the Asymmetric Unit. J. Appl. Cryst. 2006, 39, 728–734. DOI:10.1107/S0021889806028548. (c) Caliandro,R.; Carrozzini, B.; Cascarano, G. L.; De Caro, L.; Giacovazzo, C.; Mazzone, A.;Siliqi, D. Ab Initio Phasing of Proteins with Heavy Atoms atNon-Atomic Resolution: Pushing the Size Limit of Solvable Structures up to 7890Non-H Atoms in the Asymmetric Unit. J.Appl. Cryst. 2008, 41, 548–553. DOI: 10.1107/S002188980800945X.

[14] (a) Sheldrick, G. M. SHELXL-2019/3, Program forCrystal Structure Refinement, University of Göttingen, Germany, 2019. (b) Sheldrick, G. M. A Short History of SHELX. Acta Cryst. 2008, A64, 112–122. DOI: 10.1107/S0108767307043930. (c) Sheldrick, G. M. Crystal Structure Refinementwith SHELXL. Acta Cryst. 2015, C71, 3–8. DOI: 10.1107/S2053229614024218. (d) Lübben, J.; Wandtke, C. M.; Hübschle,C. B.; Ruf, M.; Sheldrick, G. M.; Dittrich, B. Aspherical scattering factorsfor SHELXL – model, implementation andapplication. Acta Cryst. 2019, A75, 50–62. DOI:10.1107/S2053273318013840.

[15] Bruker (2003). Shelxtl(Version 6.14 8/06/00). Program forStructure Solution and Refinement. Bruker AXS Inc., Madison, Wisconsin,USA.

[16] Bruker (2004). XShell(Version 6.3.1), Program for StructureRefinement. Bruker AXS Inc., Madison, Wisconsin, USA.

[17] Hübschle,C. B.; Sheldrick, G. M.; Dittrich, B. ShelXle:A Qt Graphical User Interface for SHELXL. J.Appl. Cryst. 2011, 44, 1281–1284. DOI:10.1107/S0021889811043202.

[18] McArdle, P. Oscail, A Program Package forSmall-Molecule Single-Crystal Crystallography with Crystal MorphologyPrediction and Molecular Modelling. J.Appl. Cryst. 2017, 50, 320–326. DOI: 10.1107/S1600576716018446.

[19] Farrugia, L.J. WinGX Suite for Small-MoleculeSingle-Crystal Crystallography. J. Appl.Cryst. 1999, 32, 837–838. DOI: 10.1107/S0021889899006020.

[20] Barbour, L.J. X-Seed — A Software Tool for Supramolecular Crystallography. J. Supramol. Chem. 2001, 1, 189–191. DOI: 10.1016/S1472-7862(02)00030-8.

[21] (a)Spek, A. L. Single-Crystal Structure Validation with the Program PLATON. J. Appl. Cryst. 2003, 36, 7–13. DOI: 10.1107/S0021889802022112. (b)Spek, A. L. Structure Validation in Chemical Crystallography. Acta Cryst.2009, D65, 148–155. DOI: 10.1107/S090744490804362X. (c) Spek, A. L. What Makes a Crystal StructureReport Valid? Inorg. Chim. Acta 2018, 470, 232–237. DOI:10.1016/j.ica.2017.04.036. (d)Spek, A. L. checkCIF ValidationALERTS: What They Mean and How to Respond. ActaCryst. 2020, E76, 1–11. DOI: 10.1107/S2056989019016244.

[22] Farrugia,L. J. PWT (Version 2021.2). PLATON for Windows Taskbar PWT.University of Glasgow, Scotland. (https://www.chem.gla.ac.uk/~louis/software/platon/)

[23] Bruker(2014). XPREP (Version 2014/2), Program for Space Group Determination. BrukerAXS Inc., Madison, Wisconsin, USA.

[24] Bruker (1998). XP (Version 5.1), Interactive Molecular Graphics. Bruker AXS Inc.,Madison, Wisconsin, USA.

[25] Bruker (2014). XCIF(Version 2014/2), Tables Production fromSHELXTL .cif Files. Bruker AXS Inc., Madison, Wisconsin, USA.

[26] Kratzerts, D. FinalCif(Version 115). A Full-Featured CIF FileEditor. https://dkratzert.de/finalcif.html.

[27] Allen, F. H.,Johnson, O., Shields, G. P., Smith, B. R.; Towler, M. CIF Applications. XV. enCIFer: A Program for Viewing, Editingand Visualizing CIFs. J. Appl. Cryst.2004, 37, 335–338. DOI: 10.1107/S0021889804003528.

[28] Westrip,S. P. publCIF: Software for Editing,Validating and Formatting Crystallographic Information Files. J. Appl. Cryst. 2010, 43, 920–925. DOI: 10.1107/S0021889810022120.

ChargeFlipping翻译为“正负交替反转法”参考自文献如下文献：

Wu, J.-S.; Koch, C. T.; Spence, J. C. H. IterativePhase Retrieval for Electron Diffraction Patterns by the Charge FlippingAlgorithm. J. Chin. Electr. Microsc. Soc.2007, 26, 520–527. DOI:10.3969/j.issn.1000-6281.2007.06.002.