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 paper, the local structure in the colossal thermal expansion material Ag$_3$[Co(CN)$_6$] is studied using a combination of neutron total scattering and reverse Monte Carlo (RMC) analysis.
Abstract: Local structure in the colossal thermal expansion material Ag$_3$[Co(CN)$_6$] is studied here using a combination of neutron total scattering and reverse Monte Carlo (RMC) analysis. We show that the large thermal variations in cell dimensions occur with minimal distortion of the [Co(CN)$_6$] coordination polyhedra, but involve significant flexing of the Co--CN--Ag--NC--Co linkages. We find real-space evidence in our RMC configurations for the importance of low-energy rigid unit modes (RUMs), particularly at temperatures below 150 K. Using a reciprocal-space analysis we present the phonon density of states at 300 K and show that the lowest-frequency region is dominated by RUMs and related modes. We also show that thermal variation in the energies of Ag$...$Ag interactions is evident in both the Ag partial pair distribution function and in the Ag partial phonon density of states. These findings are discussed in relation to the thermodynamic properties of the material.
38 citations
01 Apr 1999
TL;DR: Two different polyphenylene ethynylene derivatives, one partly hydrophobic and one hydrophilic, were investigated with a combination of X-ray and light scattering techniques and hydrodynamic techniques as well as scanning force microscopy and transmission electron microscopy to elucidate their molecular structure and aggregation behavior in tetrahydrofuran and water.
Abstract: Two different polyphenylene ethynylene derivatives, one partly hydrophobic and one hydrophilic, were investigated with a combination of X-ray and light scattering techniques and hydrodynamic techniques, as well as scanning force microscopy and transmission electron microscopy to elucidate their molecular structure and aggregation behavior in tetrahydrofuran and water, respectively. It turns out that both polymers possess a rod-like molecular architecture which, however, is the basis of a cascade of aggregation steps. Both, electron microscopy and X-ray analysis support the concept of a primary back-to-back aggregation of polymer chains into cylindrically shaped aggregates with high anisometry. The thickness of these aggregates was between 4.0 and 4.5 nm. The aggregates of the hydrophobic polymer further associate into fibrils and these fibrils form clusters of globular shape, though with high internal anisometry.
38 citations
TL;DR: The application of a robust generalized linear model framework for the modelling of reflection backgrounds in X-ray diffraction images is described.
Abstract: A method for estimating the background under each reflection during integration that is robust in the presence of pixel outliers is presented. The method uses a generalized linear model approach that is more appropriate for use with Poisson distributed data than traditional approaches to pixel outlier handling in integration programs. The algorithm is most applicable to data with a very low background level where assumptions of a normal distribution are no longer valid as an approximation to the Poisson distribution. It is shown that traditional methods can result in the systematic underestimation of background values. This then results in the reflection intensities being overestimated and gives rise to a change in the overall distribution of reflection intensities in a dataset such that too few weak reflections appear to be recorded. Statistical tests performed during data reduction may mistakenly attribute this to merohedral twinning in the crystal. Application of the robust generalized linear model algorithm is shown to correct for this bias.
37 citations
TL;DR: NMR spectra of the non-exchangeable protons in 5SRNA from E. coli show the existence of two distinct conformers of the molecule which meet the operational definition of "A form" or native 5S RNA, and the conditions which interconvert the two A form conformers strongly suggest that the transition between them gives rise to the low temperature optical melting transition.
Abstract: NMR spectra of the non-exchangeable protons in 5S RNA from E. coli show the existence of two distinct conformers of the molecule which meet the operational definition of "A form" or native 5S RNA. Both are easily distinguished spectroscopically from denatured, "B form" 5S RNA. The conditions which interconvert the two A form conformers strongly suggest that the transition between them gives rise to the low temperature optical melting transition first reported in 5S RNA by Kao and Crothers (1).
37 citations
TL;DR: Single crystal X-ray diffraction of oxalic acid dihydrate H(2)C(2), at pressures up to 5.3 GPa, shows significant changes in the molecular geometries, probably accompanied by a proton migration and formation of ionic species, as predicted by periodic DFT calculations.
37 citations