A short history of SHELX

doi:10.1107/S0108767307043930

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A short history of SHELX

Journal Article•DOI•

A short history of SHELX

George M. Sheldrick¹•Institutions (1)

University of Göttingen¹

01 Jan 2008-Acta Crystallographica Section A (International Union of Crystallography)-Vol. 64, Iss: 1, pp 112-122

TL;DR: This paper could serve as a general literature citation when one or more of the open-source SH ELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.

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Abstract: 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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Journal Article•DOI•

Crystal structure refinement with SHELXL

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George M. Sheldrick¹•Institutions (1)

University of Göttingen¹

01 Jan 2015-Acta Crystallographica Section C-crystal Structure Communications

TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.

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Abstract: 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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28,425 citations

Cites background from "A short history of SHELX"

...ABIN takes two free variable numbers (Sheldrick, 2008) n1 and n2 as parameters....
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...Readers not familiar with SHELX may find it useful to look at Sheldrick (2008) before reading this paper....
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...The early history has been described by Sheldrick (2008)....
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Journal Article•DOI•

OLEX2: a complete structure solution, refinement and analysis program

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Oleg V. Dolomanov¹, Luc J. Bourhis¹, Richard J. Gildea¹, Judith A. K. Howard¹, Horst Puschmann¹ - Show less +1 more•Institutions (1)

Durham University¹

01 Apr 2009-Journal of Applied Crystallography

TL;DR: 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.

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Abstract: 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.

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19,990 citations

Cites methods from "A short history of SHELX"

...The syntax of the command line input resembles that of the XP program [part of the SHELXTL system of computer programs (Sheldrick, 2008)], whilst providing more functionality and flexibility through the use of built-in or user-defined functions and a reference to the graphical objects via the…...
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...Currently OLEX2 features our own charge-flipping (Oszlányi & Süto , 2008) structure solution routine based on the smtbx, as well as supporting SHELX (Sheldrick, 2008) structure solution programs....
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...In addition to our own smtbx-based refinement (Bourhis et al., 2009), OLEX2 also supports the SHELXL refinement program (Sheldrick, 2008)....
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...The software can import and export structural data via a number of crystallographic file formats [SHELXL model files (Sheldrick, 2008), CIF, MDL MOL, PBD, XYZ, XD master files], generate the extended structure if required, produce an output image and provide a structure refinement report....
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...The syntax of the command line input resembles that of the XP program [part of the SHELXTL system of computer programs (Sheldrick, 2008)], whilst providing more functionality and flexibility through the use of built-in or user-defined functions and a reference to the graphical objects via the selection....
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Journal Article•DOI•

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

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Paul D. Adams¹, Paul D. Adams², Pavel V. Afonine¹, Gábor Bunkóczi³, Vincent B. Chen⁴, Ian W. Davis⁴, Nathaniel Echols¹, Jeffrey J. Headd⁴, Li-Wei Hung⁵, Gary J. Kapral⁴, Ralf W. Grosse-Kunstleve¹, Airlie J. McCoy³, Nigel W. Moriarty¹, Robert D. Oeffner³, Randy J. Read³, David S. Richardson⁴, Jane S. Richardson⁴, Thomas C. Terwilliger⁵, Peter H. Zwart¹ - Show less +15 more•Institutions (5)

Lawrence Berkeley National Laboratory¹, University of California, Berkeley², University of Cambridge³, Duke University⁴, Los Alamos National Laboratory⁵

01 Feb 2010-Acta Crystallographica Section D-biological Crystallography

TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.

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Abstract: 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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18,531 citations

Cites methods from "A short history of SHELX"

...…Search; Grosse-Kunstleve & Adams, 2003) combines the multi-trial dual-space recycling approaches pioneered by Shake-and-Bake (Miller et al., 1994) and later SHELXD (Sheldrick, 2008) with the use of the fast translation function (Navaza & Vernoslova, 1995; GrosseKunstleve & Brunger, 1999)....
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...The fast translation function is the basis for a systematic search in the Patterson function (performed in reciprocal space), in contrast to the stochastic alternative of SHELXD (performed in direct space)....
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...The substructure-determination procedure implemented as phenix.hyss (Hybrid Substructure Search; Grosse-Kunstleve & Adams, 2003) combines the multi-trial dual-space recycling approaches pioneered by Shake-and-Bake (Miller et al., 1994) and later SHELXD (Sheldrick, 2008) with the use of the fast translation function (Navaza & Vernoslova, 1995; GrosseKunstleve & Brunger, 1999)....
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Journal Article•DOI•

SHELXT - Integrated space-group and crystal- structure determination

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George M. Sheldrick¹•Institutions (1)

University of Göttingen¹

01 Jan 2015-Acta Crystallographica Section A

TL;DR: This work automates routine small-molecule structure determination starting from single-crystal reflection data, the Laue group and a reasonable guess as to which elements might be present.

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Abstract: The new computer program SHELXT employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group P1. Missing data are taken into account and the resolution extended if necessary. All space groups in the specified Laue group are tested to find which are consistent with the P1 phases. After applying the resulting origin shifts and space-group symmetry, the solutions are subject to further dual-space recycling followed by a peak search and summation of the electron density around each peak. Elements are assigned to give the best fit to the integrated peak densities and if necessary additional elements are considered. An isotropic refinement is followed for non-centrosymmetric space groups by the calculation of a Flack parameter and, if appropriate, inversion of the structure. The structure is assembled to maximize its connectivity and centred optimally in the unit cell. SHELXT has already solved many thousand structures with a high success rate, and is optimized for multiprocessor computers. It is, however, unsuitable for severely disordered and twinned structures because it is based on the assumption that the structure consists of atoms.

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17,039 citations

Cites methods from "A short history of SHELX"

...This structure was published by Barkley et al. (2011) in the noncentrosymmetric space group P62c, but there are two warning signs: checkCIF (Spek, 2009) detects an inversion centre (a B alert) and the Flack parameter is dubious: the current SHELXL (Sheldrick, 2015) gives a value of 0.46 (11)....
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...This is similar to the CGLS refinement in SHELXL (Sheldrick, 2008, 2015) and is performed in parallel....
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Journal Article•DOI•

VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data

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Koichi Momma¹, Fujio Izumi¹•Institutions (1)

National Institute for Materials Science¹

01 Dec 2011-Journal of Applied Crystallography

TL;DR: VESTA has been upgraded to the latest version, VESTA 3, implementing new features including drawing the external morphology of crystals, and an extended bond-search algorithm to enable more sophisticated searches in complex molecules and cage-like structures.

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Abstract: VESTA is a three-dimensional visualization system for crystallographic studies and electronic state calculations. It has been upgraded to the latest version, VESTA 3, implementing new features including drawing the external morphology of crystals; superimposing multiple structural models, volumetric data and crystal faces; calculation of electron and nuclear densities from structure parameters; calculation of Patterson functions from structure parameters or volumetric data; integration of electron and nuclear densities by Voronoi tessellation; visualization of isosurfaces with multiple levels; determination of the best plane for selected atoms; an extended bond-search algorithm to enable more sophisticated searches in complex molecules and cage-like structures; undo and redo in graphical user interface operations; and significant performance improvements in rendering isosurfaces and calculating slices.

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15,053 citations

Cites methods from "A short history of SHELX"

...File formats newly supported are GSAS *.exp files (Larson & Von Dreele, 2004), SHELX *.ins files (Sheldrick, 2008), files output by STRUCTURE TIDY (*.sto) (Gelato & Parthé, 1987), and structure and charge-density data output by CASTEP (*.cell and *.charg_frm) (Segall et al., 2002; Clark et al.,…...
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References

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Journal Article•DOI•

On the application of the minimal principle to solve unknown structures

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Russ Miller, G. DeTitta, Robert O. Jones, David A. Langs, Charles M. Weeks, Herbert A. Hauptman - Show less +2 more

05 Mar 1993-Science

TL;DR: This report focuses on algorithmic and parametric optimizations of Shake-and-Bake and the determination of two previously unknown structures that contain 105 and 110 non-hydrogen atoms, respectively.

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Abstract: The Shake-and-Bake method of structure determination is a new direct methods phasing algorithm based on a minimum-variance, phase invariant residual, which is referred to as the minimal principle. Previously, the algorithm had been applied only to known structures. This algorithm has now been applied to two previously unknown structures that contain 105 and 110 non-hydrogen atoms, respectively. This report focuses on (i) algorithmic and parametric optimizations of Shake-and-Bake and (ii) the determination of two previously unknown structures. Traditional tangent formula phasing techniques were unable to unravel these two new structures.

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142 citations

"A short history of SHELX" refers methods in this paper

...A major difference between SHELXD and SnB was the extensive use made of the Patterson function in SHELXD, both to provide better than random starting phases for the dual-space recycling and as a figure of merit....
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...The direct-methods program SHELXD (Sheldrick, 1998; Usón & Sheldrick, 1999; Sheldrick et al., 2001) was based on the dual-space (Shake and Bake) strategy introduced in the program SnB (Miller et al., 1993, 1994; Sheldrick et al., 2001); for this reason, the first beta-test version of SHELXD was referred to as half-baked....
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...Although several other powerful and user-friendly direct-methods programs are now available, for example SnB (Miller et al., 1993, 1994), SIR (Burla et al., 2005) and SHELXD (Usón & Sheldrick, 1999), that can solve much larger structures and also obtain more complete solutions, SHELXS is still…...
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...Similar tables can be made for the programs SnB (Miller et al., 1993, 1994) and SIR (Burla et al., 2005) that are at least as effective....
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...Although several other powerful and user-friendly direct-methods programs are now available, for example SnB (Miller et al., 1993, 1994), SIR (Burla et al., 2005) and SHELXD (Usón & Sheldrick, 1999), that can solve much larger structures and also obtain more complete solutions, SHELXS is still widely used....
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Journal Article•DOI•

On the use of least-squares restraints for origin fixing in polar space groups

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H. D. Flack, D. Schwarzenbach

01 Jul 1988-Acta Crystallographica Section A

TL;DR: In this article, the authors developed the theory of fixing the origin of the coordinate system in a polar space group by use of restraints (soft constraints or pseudoobservations) for any space group in any setting.

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Abstract: The theory of fixing the origin of the coordinate system in a polar space group by use of restraints (soft constraints or pseudo-observations) is developed for any space group in any setting. The coefficients of the optimal restraint equation are on the average proportional to the square of the atomic numbers. They are determined directly from the unrestrained singular normal-equations matrix. Application of the restraint results in a positive-definite matrix which is as nearly diagonal as possible for the atomic positional coordinates along the origin-free axes. Correlations between these coordinates are therefore minimized. A very compact completely general and easily implemented algorithm results which functions without user intervention.

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130 citations

Book Chapter•DOI•

[37] Patterson superposition and ab initio phasing

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George M. Sheldrick

01 Jan 1997-Methods in Enzymology

TL;DR: This chapter presents the possibility of the ab initio solution of macromolecular structures, given two unusually favorable circumstances: the availability of very high-resolution data and the presence of one or more heavier atoms, such as transition metals or even sulfur.

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Abstract: Publisher Summary This chapter presents the possibility of the ab initio solution of macromolecular structures, given two unusually favorable circumstances: the availability of very high-resolution data and the presence of one or more heavier atoms, such as transition metals or even sulfur. Under ab initio , the solution of a structure from the single-wavelength native data can be understood without the use of a known structure as a search model. Automated heavy-atom location via the Patterson function provides an efficient approach in small-molecule crystallography. For unequal atom structures involving atoms on special positions or pseudosymmetry, Patterson-based methods are often more effective than direct methods. In the case of macromolecules, the Patterson approach can be used to locate the heavier atoms, which then provide slightly better than random phases for partial structure expansion by direct or indirect methods.

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123 citations

"A short history of SHELX" refers methods in this paper

...In SHELXS-90, this was replaced by a more powerful algorithm that made extensive use of the Patterson superposition minimum function (Buerger, 1959; Richardson & Jacobson, 1987); a detailed description of the algorithm was given by Sheldrick (1991, 1997)....
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Journal Article•DOI•

Ab initio determination of the crystal structure of cytochrome c6 and comparison with plastocyanin

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Carlos Frazão, Cláudio M. Soares, Maria Arménia Carrondo¹, Ehmke Pohl², Z. Dauter, Keith S. Wilson, M. Hervés³, José A. Navarro³, M. A. De la Rosa³, George M. Sheldrick² - Show less +6 more•Institutions (3)

Instituto Superior Técnico¹, University of Göttingen², Spanish National Research Council³

01 Nov 1995-Structure

TL;DR: The determination of the structure of cytochrome c6 from the green alga Monoraphidium braunii is reported, probably the most precise structure of a heme protein to date.

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120 citations

"A short history of SHELX" refers background in this paper

...A64, 112–122 the unknown structure of the protein cytochrome c6 via one Fe and three S atoms (Frazão et al., 1995)....
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Journal Article•

On the Use of Least-Squares Restraints for Origin Fixing in Polar Space Groups

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H. D. Flack, D. Schwarzenbach

01 Jan 1988-Acta Crystallographica

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116 citations

"A short history of SHELX" refers methods in this paper

...Coordinate and displacement parameter constraints are generated automatically for atoms on special positions, and floating-origin restraints are applied automatically by the method of Flack & Schwarzenbach (1988)....
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