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: Applications of structural databases in the protein crystallographic structure determination process are reviewed, using mostly examples from work carried out by the authors.
Abstract: Applications of structural databases in the protein crystallographic structure determination process are reviewed, using mostly examples from work carried out by the authors. Four application areas are discussed: model building, model refinement, model validation and model analysis.
463 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...When the method [implemented in FRODO (Jones, 1978, 1985)] was tested, it was noticed that two turns in retinol-binding protein (RBP) were very similar in structure, yet did not resemble any previously classi®ed type of turn....
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...3D, three-dimensional; CBH, cellobiohydrolase; CSD, Cambridge Structural Database; HIC-Up, Heterocompound Information Centre, Uppsala; PDB, Protein Data Bank; RBP, retinol-binding protein; RMSD, rootmean-square distance or deviation; VRML, virtual reality modelling language; WWW, World Wide Web....
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...In the original implementation in FRODO, such a skeleton had to be converted into a set of C positions, either automatically (by placing points along the skeleton at 3.8 AÊ intervals), or manually....
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TL;DR: The conclusion of this study is that, based on the natural contrast between protein and water and "Rose-criterion" image quality, one should be able to image a frozen-hydrated biological sample using XDM at a resolution of about 10 nm.
461 citations
TL;DR: A computer program to perform small-angle X-ray and neutron scattering data evaluation is presented.
Abstract: SASfit is one of the mature programs for small-angle scattering data analysis and has been available for many years. This article describes the basic data processing and analysis workflow along with recent developments in the SASfit program package (version 0.94.6). They include (i) advanced algorithms for reduction of oversampled data sets, (ii) improved confidence assessment in the optimized model parameters and (iii) a flexible plug-in system for custom user-provided models. A scattering function of a mass fractal model of branched polymers in solution is provided as an example for implementing a plug-in. The new SASfit release is available for major platforms such as Windows, Linux and MacOS. To facilitate usage, it includes comprehensive indexed documentation as well as a web-based wiki for peer collaboration and online videos demonstrating basic usage. The use of SASfit is illustrated by interpretation of the small-angle X-ray scattering curves of monomodal gold nanoparticles (NIST reference material 8011) and bimodal silica nanoparticles (EU reference material ERM-FD-102).
459 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...Scatter is a program geared towards the analysis of twodimensional data from nano- and mesoscale oriented structures (Förster et al., 2010)....
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...…of up to 70 measurements from contrast variation experiments (Kohlbrecher et al., 2006; Vavrin et al., 2009) and analysing the (model-free) integral structural parameters of 400 scattering curves for creating local contrast in SANS by dynamic nuclear polarization (van den Brandt et al., 2007)....
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TL;DR: The paradigm sustaining such vision is illustrated, based around the four pillars of Automation, Data, Environment, and Sharing, and it is believed that AiiDA's design and its sharing capabilities will encourage the creation of social ecosystems to disseminate codes, data, and scientific workflows.
446 citations
TL;DR: Several new methods are evaluated for use in the improvement of experimental phases in the framework of a classical density-modification calculation and have been implemented in a new computer program, Parrot.
Abstract: Classical density-modification techniques (as opposed to statistical approaches) offer a computationally cheap method for improving phase estimates in order to provide a good electron-density map for model building. The rise of statistical methods has lead to a shift in focus away from the classical approaches; as a result, some recent developments have not made their way into classical density-modification software. This paper describes the application of some recent techniques, including most importantly the use of prior phase information in the likelihood estimation of phase errors within a classical density-modification framework. The resulting software gives significantly better results than comparable classical methods, while remaining nearly two orders of magnitude faster than statistical methods.
434 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...An alternative implementation using spline coefficients to provide a smooth variation with resolution has been described in Cowtan (2002) (using the terms s and ! for the scale term and the width of the Gaussian)....
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...The reference-structure data are rescaled with a resolutiondependent scale function (using a smooth-spline scaling following the method of Cowtan, 2002) to match the scale of the work structure data; this resolution-dependent scaling effectively matches the Wilson B factors....
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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