OLEX2: a complete structure solution, refinement and analysis program

doi:10.1107/S0021889808042726

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OLEX2: a complete structure solution, refinement and analysis program

Journal Article•DOI•

OLEX2: a complete structure solution, refinement and analysis program

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 (International Union of Crystallography)-Vol. 42, Iss: 2, pp 339-341

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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Journal Article•DOI•

The Cambridge Structural Database

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Colin R. Groom¹, Ian J. Bruno¹, Matthew P. Lightfoot¹, Suzanna C. Ward¹•Institutions (1)

University of Cambridge¹

01 Apr 2016-Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry

TL;DR: The creation, maintenance, information content and availability of the Cambridge Structural Database (CSD), the world’s repository of small molecule crystal structures, are described.

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Abstract: The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal–organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.

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6,313 citations

Cites methods from "OLEX2: a complete structure solutio..."

...Automatic links in software used during structure determination (Dolomanov et al., 2009), the ease with which structures can be deposited, attribution of credit in the form of a DOI and continued demonstration of the value to science of depositing crystal structures (Berman et al., 2015) may help…...
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Journal Article•DOI•

PLATON SQUEEZE: a tool for the calculation of the disordered solvent contribution to the calculated structure factors

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Anthony L. Spek¹•Institutions (1)

Utrecht University¹

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

TL;DR: The SQUEEZE method is documents as an alternative means of addressing the solvent disorder issue and conveniently interfaces with the 2014 version of the least-squares refinement program SHELXL, and many twinned structures containing disordered solvents are now also treatable by SQUEEze.

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Abstract: The completion of a crystal structure determination is often hampered by the presence of embedded solvent molecules or ions that are seriously disordered. Their contribution to the calculated structure factors in the least-squares refinement of a crystal structure has to be included in some way. Traditionally, an atomistic solvent disorder model is attempted. Such an approach is generally to be preferred, but it does not always lead to a satisfactory result and may even be impossible in cases where channels in the structure are filled with continuous electron density. This paper documents the SQUEEZE method as an alternative means of addressing the solvent disorder issue. It conveniently interfaces with the 2014 version of the least-squares refinement program SHELXL [Sheldrick (2015). Acta Cryst. C71. In the press] and other refinement programs that accept externally provided fixed contributions to the calculated structure factors. The PLATON SQUEEZE tool calculates the solvent contribution to the structure factors by back-Fourier transformation of the electron density found in the solvent-accessible region of a phase-optimized difference electron-density map. The actual least-squares structure refinement is delegated to, for example, SHELXL. The current versions of PLATON SQUEEZE and SHELXL now address several of the unnecessary complications with the earlier implementation of the SQUEEZE procedure that were a necessity because least-squares refinement with the now superseded SHELXL97 program did not allow for the input of fixed externally provided contributions to the structure-factor calculation. It is no longer necessary to subtract the solvent contribution temporarily from the observed intensities to be able to use SHELXL for the least-squares refinement, since that program now accepts the solvent contribution from an external file (.fab file) if the ABIN instruction is used. In addition, many twinned structures containing disordered solvents are now also treatable by SQUEEZE. The details of a SQUEEZE calculation are now automatically included in the CIF archive file, along with the unmerged reflection data. The current implementation of the SQUEEZE procedure is described, and discussed and illustrated with three examples. Two of them are based on the reflection data of published structures and one on synthetic reflection data generated for a published structure.

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2,712 citations

Cites background from "OLEX2: a complete structure solutio..."

...…2 (F 2)], wR(F 2) and S. Programs such as SHELXL (Sheldrick, 2008, 2015), CRYSTALS (Betteridge et al., 2003), JANA (Petřı́ček et al., 2014) and OLEX2 (Dolomanov et al., 2009) offer elaborate constraint and restraint tools to handle the least-squares refinement of an atomistic disorder model of…...
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...Relatively recently, an independent implementation of the SQUEEZE concept in the OLEX2 package (Dolomanov et al., 2009) has become available....
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Journal Article•DOI•

ShelXle: a Qt graphical user interface for SHELXL

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Christian B. Hübschle¹, George M. Sheldrick¹, Birger Dittrich¹•Institutions (1)

University of Göttingen¹

01 Dec 2011-Journal of Applied Crystallography

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.

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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.

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2,587 citations

Cites background from "OLEX2: a complete structure solutio..."

...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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...Like OLEX2 (Dolomanov et al., 2009), ShelXle is equipped with a refinement history, where every refinement step is saved and repre- 1282 Christian B. Hübschle et al. ShelXle J. Appl....
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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 Article•DOI•

Magnetic hysteresis up to 80 kelvin in a dysprosium metallocene single-molecule magnet

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Fu-Sheng Guo¹, Benjamin M. Day¹, Benjamin M. Day², Yan-Cong Chen³, Ming-Liang Tong³, Akseli Mansikkamäki⁴, Richard A. Layfield¹ - Show less +3 more•Institutions (4)

University of Sussex¹, University of Manchester², Sun Yat-sen University³, University of Jyväskylä⁴

21 Dec 2018-Science

TL;DR: A dysprosium compound is reported that manifests magnetic hysteresis at temperatures up to 80 kelvin, which overcomes an essential barrier toward the development of nanomagnet devices that function at practical temperatures.

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Abstract: Single-molecule magnets (SMMs) containing only one metal center may represent the lower size limit for molecule-based magnetic information storage materials. Their current drawback is that all SMMs require liquid-helium cooling to show magnetic memory effects. We now report a chemical strategy to access the dysprosium metallocene cation [(CpiPr5)Dy(Cp*)]+ (CpiPr5 = penta-iso-propylcyclopentadienyl, Cp* = pentamethylcyclopentadienyl), which displays magnetic hysteresis above liquid-nitrogen temperatures. An effective energy barrier to reversal of the magnetization of Ueff = 1,541 cm–1 is also measured. The magnetic blocking temperature of TB = 80 K for this cation overcomes an essential barrier towards the development of nanomagnet devices that function at practical temperatures.

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1,198 citations

Journal Article•DOI•

DIALS: implementation and evaluation of a new integration package

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Graeme Winter, David G. Waterman¹, James M. Parkhurst², Aaron S. Brewster³, Richard J. Gildea, Markus Gerstel, Luis Fuentes-Montero, Melanie Vollmar, Tara Michels-Clark³, Iris D. Young³, Nicholas K. Sauter³, Gwyndaf Evans - Show less +8 more•Institutions (3)

Rutherford Appleton Laboratory¹, Laboratory of Molecular Biology², Lawrence Berkeley National Laboratory³

01 Feb 2018-Acta Crystallographica Section D-biological Crystallography

TL;DR: A new X-ray diffraction data-analysis package is presented with a description of the algorithms and examples of its application to biological and chemical crystallography.

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Abstract: The DIALS project is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop a new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. The design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.

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733 citations

Cites methods from "OLEX2: a complete structure solutio..."

...Structure solution with SHELXT (Sheldrick, 2015) was straightforward and refinement with OLEX2 (Dolomanov et al., 2009) gave a final R1 of 3.04% (details are given in Table 2)....
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References

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Journal Article•DOI•

A short history of SHELX

[...]

George M. Sheldrick¹•Institutions (1)

University of Göttingen¹

01 Jan 2008-Acta Crystallographica Section A

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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81,116 citations

"OLEX2: a complete structure solutio..." refers methods in this paper

...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....
[...]

Journal Article•DOI•

SIR97: a new tool for crystal structure determination and refinement

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Angela Altomare¹, Maria Cristina Burla, Mercedes Camalli, Giovanni Luca Cascarano¹, Carmelo Giacovazzo¹, Antonietta Guagliardi¹, Anna Moliterni¹, Giampiero Polidori, Riccardo Spagna - Show less +5 more•Institutions (1)

University of Bari¹

01 Feb 1999-Journal of Applied Crystallography

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.

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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.

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8,807 citations

Additional excerpts

...We are also working towards the support of other available structure solution programs such as SIR97 (Altomare et al., 1999)....
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Journal Article•DOI•

The crystallographic information file (CIF) : a new standard archive file for crystallography

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Sydney Hall, F.H. Allen, I.D. Brown

01 Nov 1991-Acta Crystallographica Section A

TL;DR: The specification of a new standard Crystallographic Information File (CIF) is described, based on the Self-Defining Text Archive and Retrieval (STAR) procedure, and the CIF Core Dictionary is presented in full.

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Abstract: The specification of a new standard Crystallographic Information File (CIF) is described. Its development is based on the Self-Defining Text Archive and Retrieval (STAR) procedure [Hall (1991). J. Chem. Inf. Comput. Sci. 31, 326-333]. The CIF is a general, flexible and easily extensible free-format archive file; it is human and machine readable and can be edited by a simple text editor. The CIF is designed for the electronic transmission of crystallographic data between individual laboratories, journals and databases: it has been adopted by the International Union of Crystallography as the recommended medium for this purpose. The file consists of data names and data items, together with a loop facility for repeated items. The data names, constructed hierarchically so as to form data categories, are self-descriptive within a 32-character limit. The sorted list of data names, together with their precise definitions, constitutes the CIF Dictionary (Core Version 1991). The CIF Core Dictionary is presented in full and covers the fundamental and most commonly used data items relevant to crystal structure analysis. The Dictionary is also available as an electronic file suitable for CIF computer applications. Future extensions to the Dictionary will include data items used in more specialized areas of crystallography.

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425 citations

"OLEX2: a complete structure solutio..." refers background in this paper

...There is a CIF (crystallographic information file; Hall et al., 1991) metadata module in the OLEX2 GUI, which helps with data harvesting and report generation....
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Journal Article•DOI•

On the orthogonal transformation used for structural comparisons

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S. K. Kearsley

01 Feb 1989-Acta Crystallographica Section A

TL;DR: In this article, a constrained least-squares procedure is used to find a rotation matrix that minimizes or maximizes the sum of the squared distances between corresponding atoms for two structures.

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Abstract: Rotation matrices that minimize or maximize the sum of the squared distances between corresponding atoms for two structures are found using a constrained least-squares procedure solved analytically as an eigenvalue problem in quaternion parameters.

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268 citations

"OLEX2: a complete structure solutio..." refers methods in this paper

...Other tools include fragment matching and alignment (Kearsley, 1989)....
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Journal Article•DOI•

The charge flipping algorithm

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G. Oszlányi¹, András Sütő¹•Institutions (1)

Hungarian Academy of Sciences¹

01 Jan 2008-Acta Crystallographica Section A

TL;DR: The paper describes and compares new variants of the iteration scheme, helps to identify and improve solutions, discusses the required data and the use of known information, and tries to foretell the future of such an alternative among well established direct methods.

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Abstract: This paper summarizes the current state of charge flipping, a recently developed algorithm of ab initio structure determination. Its operation is based on the perturbation of large plateaus of low electron density but not directly on atomicity. Such a working principle radically differs from that of classical direct methods and offers complementary applications. The list of successful structure-solution cases includes periodic and aperiodic crystals using single-crystal and powder diffraction data measured with X-ray and neutron radiation. Apart from counting applications, the paper mainly deals with algorithmic issues: it describes and compares new variants of the iteration scheme, helps to identify and improve solutions, discusses the required data and the use of known information. Finally, it tries to foretell the future of such an alternative among well established direct methods.

...read moreread less

195 citations

"OLEX2: a complete structure solutio..." refers methods in this paper

...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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