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: In this paper, a generalized index of polydispersity for symmetric particles, PDI = BRg4/(1.62G), where G is the Guinier prefactor, is introduced and compared with other approaches to describe particle size distributions in SAXS, specifically the maximumentropy method.
Abstract: Control and quantification of particle size distribution is of importance in the application of nanoscale particles. For this reason, polydispersity in particle size has been the focus of many simulations of particle growth, especially for nanoparticles synthesized from aerosols such as fumed silica, titania and alumina. Single-source aerosols typically result in close to a log-normal distribution in size and micrograph evidence generally supports close to spherical particles, making such particles ideal candidates for considerations of polydispersity. Small-angle X-ray scattering (SAXS) is often used to measure particle size in terms of the radius of gyration, Rg, using Guinier's law, as well as particle surface area, S/V, from the Porod constant B and the scattering invariant Q. In this paper, the unified function is used to obtain these parameters and various moments of the particle size distribution are calculated. The particle size obtained from BET analysis of gas adsorption data directly agrees with the moment calculated from S/V. Scattering results are also compared with TEM particle-counting results. The potential of scattering to distinguish between polydisperse single particles and polydisperse particles in aggregates is presented. A generalized index of polydispersity for symmetric particles, PDI = BRg4/(1.62G), where G is the Guinier prefactor, is introduced and compared with other approaches to describe particle size distributions in SAXS, specifically the maximum-entropy method.
331 citations
TL;DR: A modification of MolScript is presented which contains the capability of the original MolScript, the ability to carry out a majority of the options available in most other crystallographic visualization packages, as well as several new features of its own.
Abstract: Macromolecular visualization is hampered by the fragmented set of available programs and the lack of cooperativity among them. The amount of visual information required for robust structural analysis is relatively difficult to generate and rarely allows further high-quality three-dimensional graphic rendering. Here, a modification of MolScript [Kraulis (1991). J. Appl. Cryst. 24, 946–950] is presented which contains the capability of the original MolScript, the ability to carry out a majority of the options available in most other crystallographic visualization packages, as well as several new features of its own. POVScript+ (currently version 1.62) allows anisotropic displacement ellipsoid rendering (read in as a second-rank tensor from a PDB file), electron-density polygonization (in several formats derived from a `marching tetrahedra' approach), volumetric rendering of electron density and GRASP/MSMS surface-map input/output. Finally, POVRay output is supported (via a modified version of PovScript) to generate high-quality renderings that are easily modified for any of a number of purposes (e.g. animations or altered textures). POVScript+ provides a marked increase in the amount of structural and atomic detail possible, while still allowing a straightforward means of generating this information.
311 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...POVScript+ features All of the POVScript+ features have been incorporated into the most current version of MolScript (version 2.1.2) (Kraulis, 1991)....
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...This feature generates a pseudo-molecular surface appearance, to which any MolScript coloring scheme can be applied (Fig....
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...Although POVRay is not interactive, the POVScript+ OpenGL interface (mostly based on the original MolScript) allows previews of most of the provided graphics features, and any manipulation performed in the OpenGL mode can be saved and transmitted to the POVRay engine in a seamless manner....
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...POVRay support Persistence of Vision Raytracing (POVRay) support in MolScript was initially added through PovScript (Peisach, 2002)....
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...POVScript+ has implemented code from and therefore offers thanks to: Per Kraulis (original MolScript author), Paul Bourke (`marching tetrahedra' algorithm), Dan Peisach and Eric Fontano (original PovScript implementation) and Nicolas Calimet (GRASP input/ output code)....
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TL;DR: CIF.iotbx.cif is a comprehensive toolbox for the development of applications that make use of the CIF format.
Abstract: iotbx.cif is a new software module for the development of applications that make use of the CIF format. Comprehensive tools are provided for input, output and validation of CIFs, as well as for interconversion with high-level cctbx [Grosse-Kunstleve, Sauter, Moriarty & Adams (2002). J. Appl. Cryst. 35, 126–136] crystallographic objects. The interface to the library is written in Python, whilst parsing is carried out using a compiled parser, combining the performance of a compiled language (C++) with the benefits of using an interpreted language.
308 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...Several CIF programming libraries have been developed for various languages and environments, including Fortran (Hall & Bernstein, 1996; Rodriguez-Carvajal & González-Platas, 2003), C (Ellis & Bernstein, 2001; Westbrook et al., 1997), Objective C (Chang & Bourne, 1998), ....
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...The interface to the library is written in Python, whilst parsing is carried out using a compiled parser, combining the performance of a compiled language (C++) with the benefits of using an interpreted language....
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TL;DR: The basic causes of the radiation damage inflicted on macromolecular crystals during diffraction experiments are summarized, as well as the current state of research which attempts to understand and to mitigate it.
Abstract: Radiation damage inflicted during diffraction data collection in macromolecular crystallography has re-emerged in the last decade as a major experimental and computational challenge, as even for crystals held at 100 K it can result in severe data-quality degradation and the appearance in solved structures of artefacts which affect biological interpretations. Here, the observable symptoms and basic physical processes involved in radiation damage are described and the concept of absorbed dose as the basic metric against which to monitor the experimentally observed changes is outlined. Investigations into radiation damage in macromolecular crystallography are ongoing and the number of studies is rapidly increasing. The current literature on the subject is compiled as a resource for the interested researcher.
305 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...Arndt (1984), Gonzalez & Nave (1994), Murray et al. (2004), Weiss et al. (2005), Shimizu et al. (2007) Is it beneficial to change/regulate the dose/dose-rate regime?...
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TL;DR: The macromolecular crystallography beamline MX1 at the Australian Synchrotron is described.
Abstract: MX1 is a bending-magnet crystallography beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the energy range from 8 to 18 keV to a focal spot at the sample position of 120 µm FWHM. The beamline endstation and ancillary equipment facilitate local and remote access for both chemical and biological macromolecular crystallography. Here, the design of the beamline and endstation are discussed. The beamline has enjoyed a full user program for the last seven years and scientific highlights from the user program are also presented.
305 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...Collection of a single diffraction image triggers indexing by the program LabelIt (Sauter et al., 2004)....
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References
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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
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
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
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
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.
Abstract: Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.
17,755 citations