scispace - formally typeset

Journal ArticleDOI

A short history of SHELX

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.

AbstractAn 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.

...read more

Content maybe subject to copyright    Report


Citations
More filters
Journal ArticleDOI
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.

21,137 citations


Cites background from "A short history of SHELX"

  • ...ABIN takes two free variable numbers (Sheldrick, 2008) n1 and n2 as parameters....

    [...]

  • ...Readers not familiar with SHELX may find it useful to look at Sheldrick (2008) before reading this paper....

    [...]

  • ...The early history has been described by Sheldrick (2008)....

    [...]

Journal ArticleDOI
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.

15,827 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)....

    [...]

  • ...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)....

    [...]

  • ...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)....

    [...]

Journal ArticleDOI
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.

14,922 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…...

    [...]

  • ...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....

    [...]

  • ...In addition to our own smtbx-based refinement (Bourhis et al., 2009), OLEX2 also supports the SHELXL refinement program (Sheldrick, 2008)....

    [...]

  • ...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....

    [...]

  • ...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....

    [...]

Journal ArticleDOI
TL;DR: This paper reports on the current status of structure validation in chemical crystallography and describes the current state of research in this area.
Abstract: Automated structure validation was introduced in chemical crystallography about 12 years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into an easy-to-use checkCIF/PLATON web-based IUCr service. The result of a crystal structure determination has to be supplied as a CIF-formatted computer-readable file. The checking software tests the data in the CIF for completeness, quality and consistency. In addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. A validation report is generated in the form of a list of ALERTS on the issues to be corrected, checked or commented on. Structure validation has largely eliminated obvious problems with structure reports published in IUCr journals, such as refinement in a space group of too low symmetry. This paper reports on the current status of structure validation and possible future extensions.

12,245 citations


Cites methods from "A short history of SHELX"

  • ...CIF became ‘the standard’ in small-molecule crystallography with its adoption by the widely used SHELXL refinementsoftware package (Sheldrick, 2008)....

    [...]

  • ...Nowadays, with twodimensional detector data, a correction for absorption is mostly of the multi-scan type (e.g. SADABS; Sheldrick, 2008) convoluted with inter-image scaling and optionally preceded by a numerical correction for absorption on the basis of a description of the crystal shape....

    [...]

Journal ArticleDOI
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.

11,698 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)....

    [...]

  • ...This is similar to the CGLS refinement in SHELXL (Sheldrick, 2008, 2015) and is performed in parallel....

    [...]


References
More filters
Journal ArticleDOI
TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
Abstract: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as `Coot'.

24,547 citations


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

  • ...Coot (Emsley & Cowtan, 2004) can create this map directly from the SHELXL .fcf file (created using the LIST 6 instruction) and can also read and write the SHELXL .res and .ins files....

    [...]

  • ...A64, 112–122 George M. Sheldrick A short history of SHELX 117 deposition), name.fcf [a CIF format file containing observed and calculated structure factors, suitable for direct input into a graphics program such as Coot (Emsley & Cowtan, 2004)] and name.pdb (PDB output)....

    [...]

  • ...Although many of the options in SHELXPRO have been made obsolete by better verification tools and Coot (Emsley & Cowtan, 2004), it is still recommended for interconverting PDB and SHELX format files and preparing the first SHELXL refinement job....

    [...]

Journal ArticleDOI
Abstract: A number of extensions to the multisolution approach to the crystallographic phase problem are discussed in which the negative quartet relations play an important role. A phase annealing method, related to the simulated annealing approach in other optimization problems, is proposed and it is shown that it can result in an improvement of up to an order of magnitude in the chances of solving large structures at atomic resolution. The ideas presented here are incorporated in the program system SHELX-90; the philosophical and mathematical background to the direct-methods part (SHELXS) of this system is described.

14,619 citations

Journal ArticleDOI
Abstract: The behaviour of Rogers's η parameter for enantiomorph-polarity estimation is examined theoretically and experimentally on simulated intensity data for seven well-assorted compounds. An alternative parameter x, based on incoherent scattering from twin components related by a centre of symmetry, is also considered. It is found that both parameters are very well adapted to implementation in a least-squares program and converge well. The η parameter can give false and over-precise indications of chirality-polarity for structures which are nearly centrosymmetric, whereas the x parameter does not have this fault and converges more rapidly than η.

9,824 citations


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

  • ...This possesses the flexibility necessary for handling merohedral and non-merohedral twins and enables a racemic twinning parameter to be refined to establish the correct absolute configuration (Flack, 1983)....

    [...]

Journal ArticleDOI
10 Mar 1970

8,159 citations


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

  • ...These days such padding is less desirable and there are excellent programs such as enCIFer (Allen et al., 2004) for working with CIF files, so CIFTAB is now effectively redundant....

    [...]

Journal ArticleDOI
15 Feb 2003-Proteins
TL;DR: Geometrical validation around the Cα is described, with a new Cβ measure and updated Ramachandran plot, and Favored and allowed ϕ,ψ regions are also defined for Pro, pre‐Pro, and Gly (important because Gly ϕ‐ψ angles are more permissive but less accurately determined).
Abstract: Geometrical validation around the Calpha is described, with a new Cbeta measure and updated Ramachandran plot. Deviation of the observed Cbeta atom from ideal position provides a single measure encapsulating the major structure-validation information contained in bond angle distortions. Cbeta deviation is sensitive to incompatibilities between sidechain and backbone caused by misfit conformations or inappropriate refinement restraints. A new phi,psi plot using density-dependent smoothing for 81,234 non-Gly, non-Pro, and non-prePro residues with B < 30 from 500 high-resolution proteins shows sharp boundaries at critical edges and clear delineation between large empty areas and regions that are allowed but disfavored. One such region is the gamma-turn conformation near +75 degrees,-60 degrees, counted as forbidden by common structure-validation programs; however, it occurs in well-ordered parts of good structures, it is overrepresented near functional sites, and strain is partly compensated by the gamma-turn H-bond. Favored and allowed phi,psi regions are also defined for Pro, pre-Pro, and Gly (important because Gly phi,psi angles are more permissive but less accurately determined). Details of these accurate empirical distributions are poorly predicted by previous theoretical calculations, including a region left of alpha-helix, which rates as favorable in energy yet rarely occurs. A proposed factor explaining this discrepancy is that crowding of the two-peptide NHs permits donating only a single H-bond. New calculations by Hu et al. [Proteins 2002 (this issue)] for Ala and Gly dipeptides, using mixed quantum mechanics and molecular mechanics, fit our nonrepetitive data in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage).

3,666 citations


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

  • ...…were deliberately left out so that backbone and side-chain torsion angles could be used for verification purposes, e.g. using the molprobity (Lovell et al., 2003) server at http://molprobity.biochem.duke.edu/, but this verification shows, especially for refinements against twinned data at…...

    [...]

  • ...Verification of the geometry with e.g. molprobity (Lovell et al., 2003) plus warning signs from a SHELXL refinement indicate where the model may need changing or alternative conformations included....

    [...]