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Journal ArticleDOI

WinGX suite for small-molecule single-crystal crystallography

01 Aug 1999-Journal of Applied Crystallography (International Union of Crystallography)-Vol. 32, Iss: 4, pp 837-838
TL;DR: The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and signi®cant updates to existing ones.
Abstract: The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and signi®cant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should follow the standard format given on page 189 of the June 1985 issue of the Journal [J. Appl. Cryst. (1985). 18, 189± 190] and on the World Wide Web at http://www.iucr. org/journals/jac/software/. Lists of software presented and/or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known.
Citations
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Journal ArticleDOI
TL;DR: The WinGX suite provides a complete set of programs for the treatment of small-molecule single-crystal diffraction data, from data reduction and processing, structure solution, model refinement and visualization, and metric analysis of molecular geometry and crystal packing, to final report preparation in the form of a CIF.
Abstract: The WinGX suite provides a complete set of programs for the treatment of small-molecule single-crystal diffraction data, from data reduction and processing, structure solution, model refinement and visualization, and metric analysis of molecular geometry and crystal packing, to final report preparation in the form of a CIF. It includes several well known pieces of software and provides a repository for programs when the original authors no longer wish to, or are unable to, maintain them. It also provides menu items to execute external software, such as the SIR and SHELX suites of programs. The program ORTEP for Windows provides a graphical user interface (GUI) for the classic ORTEP program, which is the original software for the illustration of anisotropic displacement ellipsoids. The GUI code provides input capabilities for a wide variety of file formats, and extra functionality such as geometry calculations and ray-traced outputs. The programs WinGX and ORTEP for Windows have been distributed over the internet for about 15 years, and this article describes some of the more modern features of the programs.

9,479 citations


Cites background or methods from "WinGX suite for small-molecule sing..."

  • ...The GX code was first ported to the MS-DOS environment and then to the Windows environment, becoming the WinGX program (Farrugia, 1999)....

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  • ...It was at this stage that WinGX was first publicly released on the internet in 1997 (Farrugia, 1999)....

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  • ...It now seems appropriate to describe some of the more modern features of these programs, which were not discussed in the original short computer program abstracts (Farrugia, 1997, 1999)....

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Journal ArticleDOI
TL;DR: It is found that the chemical and physical properties of these materials strongly depend on the preparation method, and the properties of the title hybrid materials with those of the "all-inorganic" CsSnI3 and CsPbI3 prepared using identical synthetic methods.
Abstract: A broad organic–inorganic series of hybrid metal iodide perovskites with the general formulation AMI3, where A is the methylammonium (CH3NH3+) or formamidinium (HC(NH2)2+) cation and M is Sn (1 and 2) or Pb (3 and 4) are reported. The compounds have been prepared through a variety of synthetic approaches, and the nature of the resulting materials is discussed in terms of their thermal stability and optical and electronic properties. We find that the chemical and physical properties of these materials strongly depend on the preparation method. Single crystal X-ray diffraction analysis of 1–4 classifies the compounds in the perovskite structural family. Structural phase transitions were observed and investigated by temperature-dependent single crystal X-ray diffraction in the 100–400 K range. The charge transport properties of the materials are discussed in conjunction with diffuse reflectance studies in the mid-IR region that display characteristic absorption features. Temperature-dependent studies show a ...

4,372 citations

Journal ArticleDOI
TL;DR: VESTA as mentioned in this paper is a cross-platform program for visualizing both structural and volumetric data in multiple windows with tabs, including isosurfaces, bird's-eye views and two-dimensional maps.
Abstract: A cross-platform program, VESTA, has been developed to visualize both structural and volumetric data in multiple windows with tabs. VESTA represents crystal structures by ball-and-stick, space-filling, polyhedral, wireframe, stick, dot-surface and thermal-ellipsoid models. A variety of crystal-chemical information is extractable from fractional coordinates, occupancies and oxidation states of sites. Volumetric data such as electron and nuclear densities, Patterson functions, and wavefunctions are displayed as isosurfaces, bird's-eye views and two-dimensional maps. Isosurfaces can be colored according to other physical quantities. Translucent isosurfaces and/or slices can be overlapped with a structural model. Collaboration with external programs enables the user to locate bonds and bond angles in the `graphics area', simulate powder diffraction patterns, and calculate site potentials and Madelung energies. Electron densities determined experimentally are convertible into their Laplacians and electronic energy densities.

4,172 citations


Cites methods from "WinGX suite for small-molecule sing..."

  • ...Electron and nuclear densities obtained with various programs including PRIMA (Izumi & Dilanian, 2002), Superflip (Palatinus & Chapuis, 2007), GSAS (Larson & Von Dreele, 2004) and WinGX (Farrugia, 1999) are directly input....

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Journal ArticleDOI
TL;DR: ShelXle is a user-friendly graphical user interface forSHELXL that combines an editor with syntax highlighting for SHELXL-associated files with an interactive graphical display for visualization of a three-dimensional structure.
Abstract: ShelXle is a graphical user interface for SHELXL [Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo–Fc) maps. Special features of ShelXle include intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions. ShelXle is completely compatible with all features of SHELXL and is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.

2,587 citations


Cites background from "WinGX suite for small-molecule sing..."

  • ...More recently, a number of excellent graphical user interfaces (GUIs) [e.g. WINGX (Farrugia, 1999), OLEX2 (Dolomanov et al., 2009), XSEED (Barbour, 2001), PLATON and SYSTEM-S (Spek, 2009), and the Bruker programs XP (Nicolet, 1981) and XSHELL (Bruker, 2000)] have been developed to facilitate…...

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  • ...More recently, a number of excellent graphical user interfaces (GUIs) [e.g. WINGX (Farrugia, 1999), OLEX2 (Dolomanov et al., 2009), XSEED (Barbour, 2001), PLATON and SYSTEM-S (Spek, 2009), and the Bruker programs XP (Nicolet, 1981) and XSHELL (Bruker, 2000)] have been developed to facilitate structure refinement with SHELXL as the underlying program, but in general the punched-card way of thinking that was central to the design of SHELXL has proven awkward to integrate into a modern interactive computer-graphics environment without losing at least some of the unique capabilities of the original program....

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Journal ArticleDOI
TL;DR: CRYSTALS as mentioned in this paper contains a modern crystallographic human-interface design, and novel strategies incorporating chemical knowledge and sensible crystallographic guidance into crystal structure analysis software, which can still only be achieved under very favourable conditions.
Abstract: The determination of small-molecule structures from single-crystal X-ray data is being carried out by researchers with little or no crys- tallographic training. At the same time, completely automatic crystal structure analysis can still only be achieved under very favourable conditions. Many of the problems that cause automatic systems to fail could be resolved with suitable chemical insight, and until this is built- in, programs continue to need human guidance. CRYSTALS version 12 contains a modern crystallographic human-interface design, and novel strategies incorporating chemical knowledge and sensible crystallographic guidance into crystal structure analysis software.

2,573 citations


Cites methods from "WinGX suite for small-molecule sing..."

  • ...CRYSTALS interfaces directly to other ®rst-class software, including PLATON (Spek, 1998), the SHELX suite (Sheldrick, 1998), SIRWARE (Altomare et al., 1999) and WinGX (Farrugia, 1999)....

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References
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Journal ArticleDOI
TL;DR: L Lists of software presented and~or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known.
Abstract: Computer Program Abstracts The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and significant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should follow the standard format given on page 189 of the June 1985 issue of the Journal [J. Appl. CrysL (1985). 18, 189190] and on the World Wide Web at http://www.iucr. ac. uk/journals/jac/software/. Lists of software presented and~or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known. J. App/. CrysL (1997). 30, 565 ORTEP-3 for Windows a version of ORTEP-III with a Graphical User Interface (GUI)

19,468 citations


"WinGX suite for small-molecule sing..." refers methods in this paper

  • ...The WinGX suite includes well established programs, such as SHELXS (Sheldrick, 1986), DIRDIF (Beurskens et al., 1996), SIR92 (Altomare et al., 1993), SHELXL93 (Sheldrick, 1993) and ORTEPIII (Johnson & Burnett, 1996; Farrugia, 1997)....

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Journal ArticleDOI
TL;DR: SIR97 is the integration of two programs, SIR92 and CAOS, the first devoted to the solution of crystal structures by direct methods, the second to refinement via least-squares–Fourier procedures.
Abstract: SIR97 is the integration of two programs, SIR92 and CAOS, the first devoted to the solution of crystal structures by direct methods, the second to refinement via least-squares–Fourier procedures. Several new features have been introduced in SIR97 with respect to the previous version, SIR92: greater automatization, increased efficiency of the direct methods section, and a powerful graphics interface. The program also provides publication tables and CIF files.

8,807 citations


"WinGX suite for small-molecule sing..." refers methods in this paper

  • ...There are inbuilt interfaces to external graphics programs, such as RasMol (Sayle & Milner-White, 1995) and SCHAKAL (Keller, 1989), and to newer programs like SHELX97 (Sheldrick, 1997) and SIR97 (Altomare et al., 1999)....

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Journal ArticleDOI
TL;DR: A least-squares procedure is described for modeling an empirical transmission surface as sampled by multiple symmetry-equivalent and/or azimuth rotation-equ equivalent intensity measurements.
Abstract: A least-squares procedure is described for modeling an empirical transmission surface as sampled by multiple symmetry-equivalent and/or azimuth rotation-equivalent intensity measurements. The fitting functions are sums of real spherical harmonic functions of even order, ylm(− u0) + ylm(u1), 2 ≤ l = 2n ≤ 8. The arguments of the functions are the components of unit direction vectors, −u0 for the reverse incident beam and u1 for the scattered beam, referred to crystal-fixed Cartesian axes. The procedure has been checked by calculations against standard absorption test data.

7,395 citations


"WinGX suite for small-molecule sing..." refers methods in this paper

  • ...Several absorption correction methods are available, e.g. analytical, Gaussian grid, scans, multiscan (Blessing, 1995), DIFABS (Walker & Stuart, 1983)....

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Journal ArticleDOI
TL;DR: In this paper, an automatic procedure for recovering a complete crystal structure after a direct phasing process is described, which consists mainly of a Fourier recycling method that can be implemented in any direct-methods package.
Abstract: An automatic procedure for recovering a complete crystal structure after a direct phasing process is described. The procedure consists mainly of a Fourier recycling method that can be implemented in any direct-methods package. The residual R value attained at the end of the process provides an estimate of the degree of success of the structure determination. The procedure can also be applied using a small molecular fragment as prior information. The procedure has been implemented into SIR92, the successor to SIR88.

4,975 citations


"WinGX suite for small-molecule sing..." refers methods in this paper

  • ...Such programs include the structuresolution packages SHELXS (Sheldrick, 1986), DIRDIF (Beurskens et al., 1996) and SIR92 (Altomare et al., 1993) and re®nement programs such as SHELXL93 (Sheldrick, 1993)....

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  • ...The WinGX suite includes well established programs, such as SHELXS (Sheldrick, 1986), DIRDIF (Beurskens et al., 1996), SIR92 (Altomare et al., 1993), SHELXL93 (Sheldrick, 1993) and ORTEPIII (Johnson & Burnett, 1996; Farrugia, 1997)....

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Journal ArticleDOI
TL;DR: In this article, a Fourier series in the polar angles of the incident and diffracted beam paths is used to model an absorption surface for the difference between the observed and calculated structure factors.
Abstract: Absorption effects usually present the most serious source of systematic error in the determination of structure factors from single-crystal X-ray diffraction measurements if the crystal is not ground to a sphere or cylinder. A novel method is proposed for the correction of these effects for data collected on a diffractometer. The method works from the premise that the manifestation of systematic errors due to absorption, unlike most other sources of systematic error, will not be evenly distributed through reciprocal space, but will be localized. A Fourier series in the polar angles of the incident and diffracted beam paths is used to model an absorption surface for the difference between the observed and calculated structure factors. Knowledge of crystal dimensions or linear absorption coefficient is not required, and the method does not necessitate the measurement of azimuthal scans or any extra data beyond the unique set. Moreover, application of the correction is not dependent upon the Laue symmetry of the crystal or the geometry of the diffractometer. The method is compared with other commonly used corrections and results are presented which demonstrate its potential.

4,930 citations


"WinGX suite for small-molecule sing..." refers methods in this paper

  • ...Several absorption correction methods are available, e.g. analytical, Gaussian grid, scans, multiscan (Blessing, 1995), DIFABS (Walker & Stuart, 1983)....

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