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•

In-house phase determination of the lima bean trypsin inhibitor: a low-resolution sulfur-SAD case.

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Judit É. Debreczeni¹, Gábor Bunkóczi¹, Beatrix Girmann¹, George M. Sheldrick¹•Institutions (1)

University of Göttingen¹

01 Feb 2003-Acta Crystallographica Section D-biological Crystallography

TL;DR: The previously unknown structure of the lima bean trypsin inhibitor (LBTI) was solved using highly redundant data collected to 3 A using a CCD detector with a rotating-anode generator and three-circle goniometer.

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Abstract: SAD (single-wavelength anomalous diffraction) has enormous potential for phasing proteins using only the anomalous signal of the almost ubiquitous native sulfur, but requires extremely precise data. The previously unknown structure of the lima bean trypsin inhibitor (LBTI) was solved using highly redundant data collected to 3 A using a CCD detector with a rotating-anode generator and three-circle goniometer. The seven `super-S' atoms (disulfide bridges) were located by dual-space recycling with SHELXD and the high solvent content enabled the density-modification program SHELXE to generate high-quality maps despite the modest resolution. Subsequently, a 2.05 A synchrotron data set was collected and used for further phase extension and structure refinement.

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31 citations

Journal Article•DOI•

1.7 A structure of the stabilized REIv mutant T39K. Application of local NCS restraints.

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Isabel Usón¹, Ehmke Pohl¹, Thomas R. Schneider, Zbigniew Dauter, Arno Schmidt¹, Hans-Joachim Fritz¹, George M. Sheldrick¹ - Show less +3 more•Institutions (1)

University of Göttingen¹

01 Jun 1999-Acta Crystallographica Section D-biological Crystallography

TL;DR: The final model has been used to perform a number of tests on anisotropic scaling, non-crystallographic symmetry, an isotropic refinement, determination of standard uncertainties and bulk solvent correction, and removal of the NCS restraints from the final model caused Rfree to increase.

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Abstract: The X-ray structure of the T39K mutant of the variable domain of a human immunoglobulin κ light chain has been determined at room temperature to 1.7 A resolution with a conventional R factor of 0.182. T39K crystallizes in the triclinic space group P1 [a = 35.4 (1), b = 40.1 (1), c = 43.1 (1) A, α = 66.9 (1), β = 85.4 (1), γ = 73.8 (1)°]. The unit-cell contains two monomers, related by a non-crystallographic twofold axis. The use of a novel type of local non-crystallographic symmetry restraints on related isotropic displacement parameters and 1–4 distances as incorporated in the refinement program SHELXL improves the model and quality of the maps, but local differences between both monomers in areas subject to different packing contacts can still be observed. 12 overall anisotropic scaling parameters were refined. These may have compensated for the difficulties in accurately scaling single rotation axis image-plate data from a triclinic crystal, because of the scarcity of common equivalent reflections. The final model has been used to perform a number of tests on anisotropic scaling, non-crystallographic symmetry, anisotropic refinement, determination of standard uncertainties and bulk solvent correction. It is remarkable that removal of the NCS restraints from the final model caused Rfree to increase. These tests clarify the strategies for optimum use of SHELXL for refinement at medium as opposed to atomic resolution.

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28 citations

Journal Article•DOI•

Serendipitous SAD phasing of an echinomycin-(ACGTACGT)2 bisintercalation complex.

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Jose A. Cuesta-Seijo¹, Manfred S. Weiss², George M. Sheldrick¹•Institutions (2)

University of Göttingen¹, European Bioinformatics Institute²

01 Apr 2006-Acta Crystallographica Section D-biological Crystallography

TL;DR: A new crystal form was obtained for the complex between (ACGTACGT)2 and echinomycin and X-ray data were collected, indicating that the two configurations are very close in energy.

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Abstract: A new crystal form was obtained for the complex between (ACGTACGT)2 and echinomycin and X-ray data were collected to 1.6 A. The structure was phased by the SAD method based on a single unexpected anomalous scatterer that could be identified as a mixture of nickel and zinc by measurements of the anomalous scattering at different wavelengths. This cation is coordinated by two guanines from two different duplexes and four water molecules. The structure resembles previously reported crystal structures of DNA–echinomycin complexes, except that three of the eight base pairs flanking the echinomycin bisintercalator sites have the Watson–Crick rather than the Hoogsteen configuration. Hoogsteen binding was found for the corresponding base pairs of the crystallographically independent duplex, indicating that the two configurations are very close in energy.

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20 citations

Journal Article•DOI•

Crystallographic computing 5: from chemistry to biology edited by D. Moras, A. D. Podjarny and J. C. Thierry

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H.M. Einspahr

01 Jan 1993-Acta Crystallographica Section A

16 citations

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

...An important feature of the output of both the SHELXS-86 and SHELXS-97 Patterson interpretation algorithms was a crossword table (Sheldrick, 1991; Schneider & Sheldrick, 2002) that tabulated, in the form of a triangular matrix, the minimum Patterson density at any vector connecting two atoms and also the minimum distance between them, in both cases taking all symmetry equivalents into account....
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...…would be timely, because most of the earlier accounts of SHELX are scattered in the excellent series of books describing the IUCr Computing Schools (Sheldrick, 1982, 1985a, 1991, 1993, 1996; Robinson & Sheldrick, 1988) that are mostly not available in computer-readable form, and later papers…...
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...An important feature of the output of both the SHELXS-86 and SHELXS-97 Patterson interpretation algorithms was a crossword table (Sheldrick, 1991; Schneider & Sheldrick, 2002) that tabulated, in the form of a triangular matrix, the minimum Patterson density at any vector connecting two atoms and…...
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...It was thought that a general overview of the SHELX system of computer programs would be timely, because most of the earlier accounts of SHELX are scattered in the excellent series of books describing the IUCr Computing Schools (Sheldrick, 1982, 1985a, 1991, 1993, 1996; Robinson & Sheldrick, 1988) that are mostly not available in computer-readable form, and later papers primarily emphasized specific macromolecular applications....
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...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•

Computing in macromolecular crystallography using a parallel architecture

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Kay Diederichs¹•Institutions (1)

University of Konstanz¹

01 Aug 2000-Journal of Applied Crystallography

TL;DR: This paper outlines the use of the OpenMP programming interface and reports its successful application for parallelization of ESSENS and SHELXL and can significantly reduce the time required for progressing from a data set to a refined model.

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Abstract: Despite advances in computer technology, computing in macromolecular crystallography keeps pace in its demand for CPU power. Improvements in CPU speed, together with advances in computing methods that depend on it, often translate into the possibility to solve structures that would otherwise require additional experiments. Programs for data reduction, molecular-replacement programs employing multidimensional searches on a grid in real, Patterson or reciprocal space, and phasing and refinement programs, currently have, among others, the highest requirements for CPU power. For these and other programs, speed-up of calculations as a result of parallel execution on multiprocessor computers is possible. This paper outlines the use of the OpenMP programming interface and reports its successful application for parallelization of ESSENS [Kleywegt & Jones (1997). Acta Cryst. D53, 179–185] and SHELXL [Schneider & Sheldrick (1997). Methods Enzymol. 277, 319–343]. Parallel computing, which is possible as a result of the inherent parallelism of crystallographic algorithms, extends the range of problems in macromolecular crystallography that programs can be applied to and can significantly reduce the time required for progressing from a data set to a refined model.

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14 citations