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Journal Article•DOI•

A short history of SHELX

George M. Sheldrick1•
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.
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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Citations
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Journal Article•DOI•
Crystal structure refinement with SHELXL

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George M. Sheldrick1•
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.
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.

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 •
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.
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.

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 •
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.
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.

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•
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.
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.

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•
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.
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.

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•
Phasing at resolution higher than the experimental resolution

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Rocco Caliandro, Benedetta Carrozzini, Giovanni Luca Cascarano, Liberato De Caro, C. Giacovazzo1, Dritan Siliqi •
National Research Council1
01 May 2005-Acta Crystallographica Section D-biological Crystallography
TL;DR: A novel procedure is presented which from an approximate electron-density map extrapolates the moduli and phases of non-measured reflections beyond and behind the experimental resolution limit, and the phase estimates of the observed reflections are subsequently improved and the interpretability of the corresponding electron- density map increases.
Abstract: Limited experimental resolution is a unavoidable feature in macromolecular crystallography: it may hinder or make difficult the determination of the crystal structure. A novel procedure is presented which from an approximate electron-density map extrapolates the moduli and phases of non-measured reflections beyond and behind the experimental resolution limit. Applications to a set of test structures show that the extrapolation can be successfully accomplished. As a consequence, the phase estimates of the observed reflections are subsequently improved and the interpretability of the corresponding electron-density map increases. The use of the extrapolated values for the non-measured reflections provides additional information for the map, which shows a resolution higher than the experimental resolution.

38 citations

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

  • ...After its incorporation in ACORN (Yao et al., 2005) and independently in SIR200X (Caliandro et al., 2005), it was also successfully added to SHELXE, where for obvious reasons it is called the free lunch algorithm....

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Journal Article•DOI•
Ab initio solution and refinement of two high-potential iron protein structures at atomic resolution.

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Emilio Parisini1, Francesco Capozzi2, Paolo Lubini1, Victor S. Lamzin3, Claudio Luchinat4, George M. Sheldrick1 •
University of Göttingen1, University of Bologna2, European Bioinformatics Institute3, University of Florence4
01 Nov 1999-Acta Crystallographica Section D-biological Crystallography
TL;DR: The unique protein molecules in H42Q-2 and rc-WT are also very similar in other respects, except for the hydrogen bonding around the mutated residue that is at the surface of the protein, supporting the hypothesis that the difference in redox potentials at lower pH values is caused primarily by differences in the charge distribution near the surface.
Abstract: The crystal structure of the reduced high-potential iron protein (HiPIP) from Chromatium vinosum has been redetermined in a new orthorhombic crystal modification, and the structure of its H42Q mutant has been determined in orthorhombic (H42Q-1) and cubic (H42Q-2) modifications. The first two were solved by ab initio direct methods using data collected to atomic resolution (1.20 and 0.93 A, respectively). The recombinant wild type (rc-WT) with two HiPIP molecules in the asymmetric unit has 1264 protein atoms and 335 solvent sites, and is the second largest structure reported so far that has been solved by pure direct methods. The solutions were obtained in a fully automated way and included more than 80% of the protein atoms. Restrained anisotropic refinement for rc-WT and H42Q-1 converged to R_1=\sum\big||F_o|-|F_c|\big|\big/\sum|F_o| of 12.0 and 13.6%, respectively [data with I>2\sigma(I)], and 12.8 and 15.5% (all data). H42Q-2 contains two molecules in the asymmetric unit and diffracted only to 2.6 A. In both molecules of rc-WT and in the single unique molecule of H42Q-1 the [Fe4S4]2+ cluster dimensions are very similar and show a characteristic tetragonal distortion with four short Fe—S bonds along four approximately parallel cube edges, and eight long Fe—S bonds. The unique protein molecules in H42Q-2 and rc-WT are also very similar in other respects, except for the hydrogen bonding around the mutated residue that is at the surface of the protein, supporting the hypothesis that the difference in redox potentials at lower pH values is caused primarily by differences in the charge distribution near the surface of the protein rather than by structural differences in the cluster region.

37 citations

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

  • ...…Å), because it provides a number of useful facilities such as the least-squares estimation of individual standard uncertainties (Cruickshank, 1999; Parisini et al., 1999), flexible treatment of disorder including the constrained refinement of occupancies, automatic constraints for atoms on…...

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Journal Article•DOI•
The antiviral antibiotic feglymycin: First direct-methods solution of a 1000 + equal-atom structure

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Gábor Bunkóczi1, Laszlo Vertesy2, George M. Sheldrick1•
University of Göttingen1, Aventis Pharma2
18 Feb 2005-Angewandte Chemie

36 citations

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

  • ...For example, the largest unknown equalatom (i.e. no atom heavier than O) structure solved using SHELXD so far is probably feglymycin (Bunkóczi et al., 2005) with 1026 unique non-H atoms....

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Journal Article•DOI•
Ab initio structure determination of the lantibiotic mersacidin.

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Thomas R. Schneider1, Jörg Kärcher1, Ehmke Pohl1, Paolo Lubini1, George M. Sheldrick1 •
University of Göttingen1
01 Jun 2000-Acta Crystallographica Section D-biological Crystallography
TL;DR: The crystal structure of mersacidin, a potential novel antibiotic against methicillin- and vancomycin-resistant Staphylococcus aureus strains, has been determined by ab initio methods and is the largest approximately equal-atom unknown structure solved by direct methods.
Abstract: The crystal structure of mersacidin, a potential novel antibiotic against methicillin- and vancomycin-resistant Staphylococcus aureus strains, has been determined by ab initio methods Despite all crystals being merohedrally twinned, an accurate structural model with an R value of 134% has been obtained at atomic resolution With six molecules in the asymmetric unit and no atom heavier than sulfur, the structure corresponds to a protein of 120 amino acids and is the largest approximately equal-atom unknown structure solved by direct methods In the crystal, the molecule assumes a compact fold different from that found by NMR in solution Comparison of the NCS-related molecules reveals regions of variable flexibility The region highly homologous to the related antibiotic actagardine is very rigid and possibly defines an essential building block of this class of new antibacterial substances

33 citations

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

  • ...Detailed descriptions of twinned refinement strategy have been given by Herbst-Irmer & Sheldrick (1998, 2002) and Schneider et al. (2000)....

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  • ...…Van der Maelen & Sheldrick (1996) and of course in Peter Müller’s book (Müller et al., 2006); the refinement of the twinned structure of mersacidin (Schneider et al., 2000) made extensive use of similar distance restraints, taking advantage of the six independent molecules in the asymmetric…...

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Journal Article•DOI•
Structure of viscotoxin A3: disulfide location from weak SAD data

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Judit É. Debreczeni1, Beatrix Girmann1, Axel Zeeck1, Ralph Krätzner1, George M. Sheldrick1 •
University of Göttingen1
01 Dec 2003-Acta Crystallographica Section D-biological Crystallography
TL;DR: An innovation in the dual-space substructure-solution program SHELXD enabled the individual S atoms of the disulfide bonds to be located using the Cu Kalpha data; this resulted in a marked improvement in the phasing compared with the use of super-S atoms.
Abstract: The crystal structure of viscotoxin A3 (VT A3) extracted from European mistletoe (Viscum album L.) has been solved using the anomalous diffraction of the native S atoms measured in-house with Cu Kα radiation to a resolution of 2.2 A and truncated to 2.5 A. A 1.75 A resolution synchrotron data set was used for phase expansion and refinement. An innovation in the dual-space substructure-solution program SHELXD enabled the individual S atoms of the disulfide bonds to be located using the Cu Kα data; this resulted in a marked improvement in the phasing compared with the use of super-S atoms. The VT A3 monomer consists of 46 amino acids with three disulfide bridges and has an overall fold resembling the canonical architecture of the α- and β-thionins, a capital letter L. The asymmetric unit consists of two monomers related by a local twofold axis and held together by hydrophobic interactions between the monomer units. One phosphate anion (confirmed by 31P-NMR and MS) is associated with each monomer.

32 citations

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