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Journal Article•DOI•

Phase annealing in SHELX-90: direct methods for larger structures

George M. Sheldrick
01 Jun 1990-Acta Crystallographica Section A (International Union of Crystallography)-Vol. 46, Iss: 6, pp 467-473
TL;DR: In this article, 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.
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.
Citations
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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
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.

81,116 citations

Journal Article•DOI•
Automated MAD and MIR structure solution

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Thomas C. Terwilliger1, Joel Berendzen1•
Los Alamos National Laboratory1
01 Apr 1999-Acta Crystallographica Section D-biological Crystallography
TL;DR: A fully automated procedure for solving MIR and MAD structures has been developed using a scoring scheme to convert the structure-solution process into an optimization problem.
Abstract: Obtaining an electron-density map from X-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because MIR and MAD structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained. A set of criteria for evaluating the quality of heavy-atom partial solutions in macromolecular crystallography have been developed. These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation. The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit. The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations.

3,091 citations

Cites methods from "Phase annealing in SHELX-90: direct..."

  • ...…structures of the heavy or anomalously scattering atoms are generally obtained either by manual or semi-automated inspection of difference Patterson functions (Terwilliger et al., 1987; Chang & Lewis, 1994; Vagin & Teplyakov, 1998) or by direct methods (Sheldrick, 1990; Miller et al., 1994)....

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Journal Article•DOI•
SIR2004: an improved tool for crystal structure determination and refinement

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Maria Cristina Burla, Rocco Caliandro, Mercedes Camalli, Benedetta Carrozzini, Giovanni Luca Cascarano, Liberato De Caro, C. Giacovazzo1, Giampiero Polidori, Riccardo Spagna •
National Research Council1
01 Apr 2005-Journal of Applied Crystallography
TL;DR: SIR2004 as mentioned in this paper is the evolution of the SIR2002 program, which is devoted to the solution of crystal structures by direct and Patterson methods, and it is able to solve ab initio both small/medium-size structures as well as macromolecules (up to 2000 atoms in the asymmetric unit).
Abstract: SIR2004 is the evolution of the SIR2002 program [Burla, Camalli, Carrozzini, Cascarano, Giacovazzo, Polidori & Spagna (2003). J. Appl. Cryst. 36, 1103]. It is devoted to the solution of crystal structures by direct and Patterson methods. Several new features implemented in SIR2004 make this program efficient: it is able to solve ab initio both small/medium-size structures as well as macromolecules (up to 2000 atoms in the asymmetric unit). In favourable circumstances, the program is also able to solve protein structures with data resolution up to 1.4–1.5 A, and to provide interpretable electron density maps. A powerful user-friendly graphical interface is provided.

2,561 citations

Cites methods from "Phase annealing in SHELX-90: direct..."

  • ...Among them we quote: SHELX-D (Sheldrick, 1998), developing the molecular model by alternating tangent refinement (i.e. the reciprocal-space search) and direct-space techniques [i.e. via the use of the iterative peak list optimization (see Sheldrick & Gould, 1995)]; ACORN (Foadi et al., 2000), locating a small fragment of the molecule (eventually by molecular replacement techniques) to obtain a useful non-random starting set of phases, and refining them successively by means of solvent flattening techniques; SIR2002 (Burla et al., 2002), which has been successfully applied to the ab initio phasing of proteins, combining the random phase approach with the tangent procedure, and using real-space techniques for refining the phases, without alternating them with reciprocal-space methods....

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  • ...…SIR92 (Altomare et al., 1994), SIR97 (Altomare et al., 1999)] have been used by many laboratories worldwide in the past 15 years, and have contributed, together with programs like MULTAN (Main et al., 1980), SHELX (Sheldrick, 1990) and RANTAN (Yao, 1981), to the solution of many crystal structures....

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  • ...The previously released programs [SIR88 (Burla et al., 1989), SIR92 (Altomare et al., 1994), SIR97 (Altomare et al., 1999)] have been used by many laboratories worldwide in the past 15 years, and have contributed, together with programs like MULTAN (Main et al., 1980), SHELX (Sheldrick, 1990) and RANTAN (Yao, 1981), to the solution of many crystal structures....

    [...]

Journal Article•DOI•
Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria

[...]

Gerry McDermott1, Stephen M. Prince1, Andrew A. Freer1, A. M. Hawthornthwaite-Lawless2, Miroslav Z. Papiz2, Richard J. Cogdell1, Neil W. Isaacs1 •
University of Glasgow1, Daresbury Laboratory2
06 Apr 1995-Nature
TL;DR: The crystal structure of the light harvesting antenna complex (LH2) from Rhodopseudomonas acidophila strain 10050 showed that the active assembly consists of two concentric cylinders of helical protein subunits which enclose the pigment molecules as discussed by the authors.
Abstract: The crystal structure of the light-harvesting antenna complex (LH2) from Rhodopseudomonas acidophila strain 10050 shows that the active assembly consists of two concentric cylinders of helical protein subunits which enclose the pigment molecules Eighteen bacteriochlorophyll a molecules sandwiched between the helices form a continuous overlapping ring, and a further nine are positioned between the outer helices with the bacteriochlorin rings perpendicular to the transmembrane helix axis There is an elegant intertwining of the bacteriochlorophyll phytol chains with carotenoid, which spans the complex

2,537 citations

Journal Article•DOI•
Substructure solution with SHELXD.

[...]

Thomas R. Schneider1, George M. Sheldrick1•
University of Göttingen1
01 Oct 2002-Acta Crystallographica Section D-biological Crystallography
TL;DR: Iterative dual-space direct methods based on phase refinement in reciprocal space and peak picking in real space are able to locate relatively large numbers of anomalous scatterers efficiently from MAD or SAD data.
Abstract: Iterative dual-space direct methods based on phase refinement in reciprocal space and peak picking in real space are able to locate relatively large numbers of anomalous scatterers efficiently from MAD or SAD data. Truncation of the data at a particular resolution, typically in the range 3.0–3.5 A, can be critical to success. The efficiency can be improved by roughly an order of magnitude by Patterson-based seeding instead of starting from random phases or sites; Patterson superposition methods also provide useful validation. The program SHELXD implementing this approach is available as part of the SHELX package.

1,620 citations

Cites background or methods from "Phase annealing in SHELX-90: direct..."

  • ...The minimal function (Miller et al., 1993), the tangent-formula residual R (Sheldrick, 1990) and the conventional R factor were also successful at identifying the correct solutions for a given structure, but not quite as useful as the correlation coef®cient as absolute ®gures of merit....

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  • ...…the Patterson function is hardly a viable option, but conventional small-molecule direct methods (Wilson, 1978; Yao, 1981; Mukherjee et al., 1989; Sheldrick, 1990) and automated computer Patterson interpretation (Sheldrick et al., 1993; Sheldrick, 1998; Terwilliger & Berendzen, 1999;…...

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References
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Book•
Crystallographic Computing 3: Data Collection, Structure Determination, Proteins and Databases

[...]

George M. Sheldrick, R. Goddard, C. Kruger
01 Dec 1985
TL;DR: The latest in a series on crystallographic computing, this collection of 33 papers covers the full spectrum of computer applications in crystallography, including the use of micro-, mini-, and mainframe computers.
Abstract: The latest in a series on crystallographic computing, this collection of 33 papers covers the full spectrum of computer applications in crystallography, including the use of micro-, mini-, and mainframe computers. Special emphasis is given to single crystal and powder data collection, including position sensitive detectors; to crystallographic databases; to computer methods in protein crystallography; and to program systems for crystal structure determination. Presented at the Ninth International School on Crystallographic Computing, held in Mulheim (FRG) in August 1984, these papers provide state-of-the-art information that is not available elsewhere.

190 citations

Journal Article•DOI•
Crystallographic Computing 4. Techniques and New Technologies

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J. Sieler
01 Jan 1989-Zeitschrift Fur Kristallographie

177 citations

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