Crystal structure refinement with SHELXL

doi:10.1107/S2053229614024218

Journal Article•DOI•

Crystal structure refinement with SHELXL

01 Jan 2015-Acta Crystallographica Section C-crystal Structure Communications (International Union of Crystallography)-Vol. 71, Iss: 1, pp 3-8

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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Journal Article•DOI•

A short history of SHELX

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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

"Crystal structure refinement with S..." refers background in this paper

...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•

Structure validation in chemical crystallography

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Anthony L. Spek¹•Institutions (1)

Utrecht University¹

01 Feb 2009-Acta Crystallographica Section D-biological Crystallography

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.

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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.

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13,163 citations

"Crystal structure refinement with S..." refers methods in this paper

...This option is essential for applying the SQUEEZE option in PLATON to twinned structures, but also has other uses....
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...For twinned structures, it is necessary first to use the new LIST 8 instruction (see below) to generate detwinned data for input to PLATON....
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...PLATON calculates the partial structure factors corresponding to a blob of unmodelled difference density and writes them to the .fab file....
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...The new ABIN instruction was primarily designed to facilitate the use of the SQUEEZE facility (Spek, 2015) in the program PLATON (Spek, 2009), but it can also be used to input a bulk solvent model for a macromolecule....
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Journal Article•DOI•

On enantiomorph‐polarity estimation

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H. D. Flack

01 Nov 1983-Acta Crystallographica Section A

TL;DR: In this article, the behaviour of the Rogers's η parameter for enantiomorph-polarity estimation is examined theoretically and experimentally on simulated intensity data for seven well-assorted compounds.

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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.

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9,932 citations

"Crystal structure refinement with S..." refers methods in this paper

...When the 2008 SHELX paper was written, the method of choice to determine the absolute structure was to refine the Flack parameter (Flack, 1983) as one of the parameters in a full-matrix refinement....
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Journal Article•DOI•

The Cambridge Structural Database: a quarter of a million crystal structures and rising

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Frank H. Allen¹•Institutions (1)

University of Cambridge¹

01 Jun 2002-Acta Crystallographica Section B-structural Science

TL;DR: The Cambridge Structural Database now contains data for more than a quarter of a million small-molecule crystal structures, and projections concerning future accession rates indicate that the CSD will contain at least 500,000 crystal structures by the year 2010.

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Abstract: The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-molecule crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chemical information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500000 crystal structures by the year 2010.

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9,865 citations

"Crystal structure refinement with S..." refers background in this paper

...…to understand why several leading chemical journals still only require the deposition of the atom coordinates, etc., but not the reflection data, especially now that the Cambridge Structural Database (CSD; Allen, 2002) accepts the new CIFs and strongly encourages deposition of the reflection data....
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Journal Article•DOI•

J. Appl. Cryst.の発刊に際して

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良二上田

10 Mar 1970

8,159 citations

"Crystal structure refinement with S..." refers methods in this paper

...Multithreading is achieved using OpenMP along the lines suggested by Diederichs (2000), and the program is particularly suitable for multiple-core processors....
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Crystal structure refinement with SHELXL

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"Crystal structure refinement with S..." refers background in this paper

"Crystal structure refinement with S..." refers methods in this paper

"Crystal structure refinement with S..." refers methods in this paper

"Crystal structure refinement with S..." refers background in this paper

"Crystal structure refinement with S..." refers methods in this paper

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