J. Appl. Cryst.の発刊に際して
10 Mar 1970-Vol. 12, Iss: 1, pp 1-1
About: The article was published on 1970-03-10 and is currently open access. It has received 8159 citations till now.
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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
Cites background from "J. Appl. Cryst.の発刊に際して"
...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....
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TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
34,239 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...This dictionary contains among oth i ems descriptions of the solution components, the experime conditions, enumerated lists of the instruments used, as we information about structure refinement....
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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.
28,425 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...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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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'.
27,505 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...…e-mail: emsley@ysbl.york.ac.uk # 2004 International Union of Crystallography Printed in Denmark ± all rights reserved 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…...
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...The introduction of FRODO (Jones, 1978) and then O (Jones et al., 1991) to the ®eld of protein crystallography was in each case revolutionary, each in their time breaking new ground in demonstrating what was possible with the current hardware....
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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.
18,531 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...After ensuring that the diffraction data are sound and understood, the next critical necessity for solving a structure is the determination of phases using one of several strategies (Adams, Afonine et al., 2009)....
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...Tools such as efficient rigid-body refinement (multiplezones algorithm; Afonine et al., 2009), simulated-annealing refinement (Brünger et al., 1987) in Cartesian or torsion-angle space (Grosse-Kunstleve et al., 2009), automatic NCS detection and its use as restraints in refinement are important at…...
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References
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TL;DR: In this article, the authors present several approaches to interpret small-angle scattering data from solutions of biological macromolecules in terms of three-dimensional models, including ab initio low-resolution shape and domain structure determination, modelling of quaternary structure by rigid-body refinement, simultaneous analysis of multiple scattering patterns, e.g. from contrast variation in neutron scattering to study multicomponent complexes, validation of high-resolution models; and addition of missing loops and domains.
Abstract: In recent years, major progress has been achieved in developing novel approaches to interpret small-angle scattering data from solutions of biological macromolecules in terms of three-dimensional models. These advanced methods include: ab initio low-resolution shape and domain structure determination; modelling of quaternary structure by rigid-body refinement; simultaneous analysis of multiple scattering patterns, e.g. from contrast variation in neutron scattering to study multicomponent complexes; validation of high-resolution models; and addition of missing loops and domains. The new techniques will be presented and practical applications of the methods are illustrated by recent examples. The use of additional information from other methods, joint applications of X-ray and neutron scattering, and the possibilities for assessing and validating the models constructed based on small-angle scattering data will be discussed.
37 citations
TL;DR: A procedure for model building is described that combines morphing a model to match a density map, trimming the morphed model and aligning the model to a sequence.
Abstract: A procedure termed `morphing' for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. The procedure was tested by application to a recently determined structure at a resolution of 3.2 A and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package.
37 citations
TL;DR: In this work, methods to quantify and thus classify the DOH of microstructures are investigated and compared and three methods are evaluated using particle packings generated by Brownian dynamics simulations: the pore size distribution, the density-fluctuation method, and the Voronoi volume distribution.
Abstract: The microstructure of coagulated colloidal particles, for which the interparticle potential is described by the Derjaguin-Landau-Verweg-Overbeek theory, is strongly influenced by the particles' surface potential. Depending on its value, the resulting microstructures are either more "homogeneous" or more "heterogeneous," at equal volume fractions. An adequate quantification of a structure's degree of heterogeneity (DOH), however, does not yet exist. In this work, methods to quantify and thus classify the DOH of microstructures are investigated and compared. Three methods are evaluated using particle packings generated by Brownian dynamics simulations: (1) the pore size distribution, (2) the density-fluctuation method, and (3) the Voronoi volume distribution. Each method provides a scalar measure, either via a parameter in a fit function or an integral, which correlates with the heterogeneity of the microstructure and which thus allows to quantitatively capture the DOH of a granular material. An analysis of the differences in the density fluctuations between two structures additionally allows for a detailed determination of the length scale on which differences in heterogeneity are most pronounced.
37 citations
TL;DR: A recently developed electron diffraction technique called D-STEM is coupled with precession electron microscopy to obtain quantitative local texture information in damascene copper interconnects with a spatial resolution of less than 5 nm, revealing strong variations in texture and grain boundary distribution of the copper lines upon downscaling.
Abstract: In this work, a recently developed electron diffraction technique called diffraction scanning transmission electron microscopy (D-STEM) is coupled with precession electron microscopy to obtain quantitative local texture information in damascene copper interconnects (1.8µm‐70 nm in width) with a spatial resolution of less than 5 nm. Misorientation and trace analysis is performed to investigate the grain boundary distribution in these lines. The results reveal strong variations in texture and grain boundary distribution of the copper lines upon downscaling. Lines of width 1.8µm exhibit a strong!111"normal texture and comprise large micron-size grains. Upon downscaling to 180 nm, a{111}!110"bi-axial texture has been observed. In contrast, narrower lines of widths 120 and 70 nm reveal sidewall growth of{111} grains and a dominant!110"normal texture. The microstructure in these lines comprises clusters of small grains separated by high angle boundaries in the vicinity of large grains. The fraction of coherent twin boundaries also reduces with decreasing line width. (Some figures may appear in colour only in the online journal)
37 citations
TL;DR: Mn(II) complexes of scorpiand-type azamacrocycles constituted by a tretrazapyridinophane core appended with an ethylamino tail including 2- or 4-quinoline functionalities show very appealing in vitro SOD activity.
37 citations