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.
Citations
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TL;DR: A computer program that automatically classifies and clusters structural fragments extracted from mining the Cambridge Structural Database is described and a set of visualization tools that enable the user to view and verify the proposed classification scheme, and further explore it in varying levels of detail.
Abstract: A computer program that automatically classifies and clusters structural fragments extracted from mining the Cambridge Structural Database is described. The methodology is based on cluster analysis and multivariate data processing of distance matrix information describing the extracted fragments. Coupled with the calculations is a set of visualization tools that enable the user to view and verify the proposed classification scheme, and further explore it in varying levels of detail. Two examples are presented: the first is based on a simple difluoroalkene fragment and the second, more complex, on a chiral vicinal dialcohol, R1(OH)CHCH(OH)R2.
36 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...…member of the cluster, i.e. for cluster J containing m patterns, the most representative sample, i, is defined as that which gives min Xm j¼1 i;j2J d i; jð Þ=m 2 64 3 75: ð5Þ (vi) Semi-independent cluster validation tools are also employed using silhouettes (Rousseeuw, 1987; Barr et al., 2004c)....
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...In previous papers (Barr et al., 2004a,b,c,d), we have shown how pattern matching coupled with cluster analysis and multivariate statistical methods can be used to classify large numbers of powder patterns, for example to identify salts and polymorphs, or to analyze round-robin type data where…...
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...The dSNAP program is a highly modified and extended version of the computer program PolySNAP (Barr et al., 2004b,c)....
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...Correspondence e-mail: chris@chem.gla.ac.uk A computer program that automatically classifies and clusters structural fragments extracted from mining the Cambridge Structural Database is described....
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...The continued increase in the number of entries in the Cambridge Structural Database (CSD; Allen, 2002) poses problems: it is an enormously powerful resource, but with more than 325000 entries, extracting meaningful chemical information can be daunting....
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TL;DR: The fixed-target approach to sample delivery involves depositing samples on a thin-film support and subsequent serial introduction via a translating stage as discussed by the authors, where the sample of interest must be serially replaced after each destructive pulse.
Abstract: X-ray free-electron lasers (XFELs) offer a new avenue to the structural probing of complex materials, including biomolecules Delivery of precious sample to the XFEL beam is a key consideration, as the sample of interest must be serially replaced after each destructive pulse The fixed-target approach to sample delivery involves depositing samples on a thin-film support and subsequent serial introduction via a translating stage Some classes of biological materials, including two-dimensional protein crystals, must be introduced on fixed-target supports, as they require a flat surface to prevent sample wrinkling A series of wafer and transmission electron microscopy (TEM)-style grid supports constructed of low-Z plastic have been custom-designed and produced Aluminium TEM grid holders were engineered, capable of delivering up to 20 different conventional or plastic TEM grids using fixed-target stages available at the Linac Coherent Light Source (LCLS) As proof-of-principle, X-ray diffraction has been demonstrated from two-dimensional crystals of bacteriorhodopsin and three-dimensional crystals of anthrax toxin protective antigen mounted on these supports at the LCLS The benefits and limitations of these low-Z fixed-target supports are discussed; it is the authors' belief that they represent a viable and efficient alternative to previously reported fixed-target supports for conducting diffraction studies with XFELs
36 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...Crystal hits were identified in the raw data and converted to HDF5 file format using Cheetah (Barty et al., 2014), and diffraction patterns were visualized using the hdfsee feature in CrystFEL (White et al., 2012)....
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TL;DR: In this paper, a model called the inverse Kroner model is proposed to calculate the diffraction elastic constants from the elastic constants of a single crystal, which is related to the classic Kroner models.
Abstract: A model, dubbed the inverse Kroner model, is proposed to calculate the diffraction elastic constants from the elastic constants of a single crystal. It is related to the classic Kroner model, and both are identified as bounds on the diffraction elastic constants. Through the grain shape as controlling parameter, the classic Kroner model is bound by the hkl-independent mechanical limit given by the bulk elastic constants of the matrix, while the inverse Kroner model approaches the Reuss limit.
36 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...Through the grain shape as controlling parameter, the classic Kröner model is bound by the hkl-independent mechanical limit given by the bulk elastic constants of the matrix, while the inverse Kröner model approaches the Reuss limit....
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...An alternative expression for Fij is developed in the following....
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TL;DR: The results obtained here compare well with estimates of these parameters obtained via analysis of electron spectroscopic results in conjunction with the Anderson impurity model, and the dependence of the hopping interaction strength t is found to be approximately $r^{-3}$.
Abstract: We have analyzed the ab initio local-density-approximation band-structure calculations for the family of perovskite oxides, $LaMO_3$ with M=Ti–Ni within a parametrized nearest-neighbor tight-binding model, and extracted various interaction strengths. We study the systematics in these interaction parameters across the transition-metal series, and discuss the relevance of these in a many-body description of these oxides. The results obtained here compare well with estimates of these parameters obtained via analysis of electron spectroscopic results in conjunction with the Anderson impurity model. The dependence of the hopping interaction strength t is found to be approximately $r^{-3}$.
36 citations
Cites background from "J. Appl. Cryst.の発刊に際して"
...Fig.6 The variation of ǫp-ǫd across the transition metals series, Ti-Ni....
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TL;DR: A simple robust manual protocol for producing crystals in the lipidic cubic phase in less than an hour is described to provide newcomers to the in meso method for crystallizing membrane proteins with experience of preparing, handling and growing crystals inThe sticky and viscous lipidic mesophase.
Abstract: A simple and inexpensive protocol for producing crystals in the sticky and viscous mesophase used for membrane protein crystallization by the in meso method is described. It provides crystals that appear within 15–30 min of setup at 293 K. The protocol gives the experimenter a convenient way of gaining familiarity and a level of comfort with the lipidic cubic mesophase, which can be daunting as a material when first encountered. Having used the protocol to produce crystals of the test protein, lysozyme, the experimenter can proceed with confidence to apply the method to more valuable membrane (and soluble) protein targets. The glass sandwich plates prepared using this robust protocol can further be used to practice harvesting and snap-cooling of in meso-grown crystals, to explore diffraction data collection with mesophase-embedded crystals, and for an assortment of quality control and calibration applications when used in combination with a crystallization robot.
36 citations
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