An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-molecule refinement and SHELXS and SHELXD are often employed for structure solution despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromolecules against high-resolution or twinned data; SHELXPRO acts as an interface for macromolecular applications. SHELXC, SHELXD and SHELXE are proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.

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A short history of SHELX

The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

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Crystal structure refinement with SHELXL

New software, OLEX2, has been developed for the determination, visualization and analysis of molecular crystal structures. The software has a portable mouse-driven workflow-oriented and fully comprehensive graphical user interface for structure solution, refinement and report generation, as well as novel tools for structure analysis. OLEX2 seamlessly links all aspects of the structure solution, refinement and publication process and presents them in a single workflow-driven package, with the ultimate goal of producing an application which will be useful to both chemists and crystallographers.

OLEX2: a complete structure solution, refinement and analysis program

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. How­ever, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallo­graphic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.

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PHENIX: a comprehensive Python-based system for macromolecular structure solution

Upon complete epoxidation of the vitamin D3 4-phenyltriazoline-3,5-dione adducts2 and3 withMCPBA, four diastereomeric bisoxiranes7, 8, 9, and10 were generated. The stereochemistry of all the chiral centers in these compounds has been established by chemical correlation with compounds of known stereochemistry and by single crystal X-ray structure determination of the benzoyl derivative10 b.

Über die Stereochemie der Bisoxirane aus den 4-N-Phenyl-triazolin-3,5-dion-addukten von Vitamin D3: Röntgenstrukturanalyse eines der Benzoylderivate

The crystal structure of the product of the reaction between bis(dimethylglyoximato)pyridinecobalt-(I) and the insecticide 1,1-bis-(p-chlorophenyl)-2,2,2-trichloroethane (p,p′-DDT) shows the presence of a chlorovinyl group σ-bonded to cobalt.

Cobaloxime and DDT. X-Ray crystal structure of an unexpected vinyl-cobalt(III) complex

The crystal structure of a complex between 2,3,11, 12-(bis-1,2-acenaphtho)-18-crown-6 and potassium isothiocyanate

The complete manuscript of this communication appears in: Angew. Chem. Suppl. 1982, 1009. DOI:10.1002/anie.198210090

A Spirocyclic Diphosphirane

The current routine procedure for publishing crystal structures of small molecules includes structure validation via the the IUCr CheckCIF service. [1] Part of that procedure is the Hirshfeld test [2] which ensures that the atomic vibrations, encoded as Atomic Displacement Parameters (ADPs), are physically reasonable. While the Hirshfeld test is fast and efficient at finding potential problems in the structural model, there exist a number of borderline cases where the test is not able to find implausible ADPs. In other cases the CheckCIF routine might raise alerts where the structure is actually perfectly fine. An improved procedure will be presented which aims to address these problems. The procedure is based on the Hirshfeld test and inspired by the 'RIGU' restraint from the Shelxl [3] program. This is achieved by analyzing the ADPs characteristics in all three spacial dimensions instead of only validating its expansion in bond direction and taking the atomic masses applied to a harmonic oscillator model into account. This procedure achieves its goal of finding problematic ADPs in cases that are not found by the traditional Hirshfeld test and is able to reasonably evaluate the ADPs of atoms with significantly different atomic masses e.g. carbon – hydrogen bonds in neutron diffraction studies. [1] Spek Acta Cryst (2015). C71, 9-18. [2] Rosenfield et al., Acta Cryst (1978). A34, 828–829. [3] Thorn et al., Acta Cryst. (2012). A68, 448-451.

https://journals.iucr.org/a/issues/2016/a1/00/a54247/a54247.pdf

George M. Sheldrick

Papers

Über die Stereochemie der Bisoxirane aus den 4-N-Phenyl-triazolin-3,5-dion-addukten von Vitamin D3: Röntgenstrukturanalyse eines der Benzoylderivate

Cobaloxime and DDT. X-Ray crystal structure of an unexpected vinyl-cobalt(III) complex

The crystal structure of a complex between 2,3,11, 12-(bis-1,2-acenaphtho)-18-crown-6 and potassium isothiocyanate

A Spirocyclic Diphosphirane

An Enhanced Hirshfeld Test - Validating Atomic Vibrations in Crystal Structures