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: A molecular-replacement procedure that uses an evolutionary algorithm to simultaneously optimize the orientation and position of a search model in a unit cell is developed and its dependence on search model quality and choice of target function is examined.
Abstract: Stochastic search algorithms can be used to perform rapid six-dimensional molecular-replacement searches. A molecular-replacement procedure has been developed that uses an evolutionary algorithm to simultaneously optimize the orientation and position of a search model in a unit cell. Here, the performance of this algorithm and its dependence on search model quality and choice of target function are examined. Although the evolutionary search procedure is capable of finding solutions with search models that represent only a small fraction of the total scattering matter of the target molecule, the efficiency of the search procedure is highly dependent on the quality of the search model. Polyalanine models frequently provide better search efficiency than all-atom models, even in cases where the side-chain positions are known with high accuracy. Although the success of the search procedure is not highly dependent on the statistic used as the target function, the correlation coefficient between observed and calculated structure-factor amplitudes generally results in better search efficiency than does the R factor. An alternative stochastic search procedure, simulated annealing, provides similar overall performance to evolutionary search. Methods of extending the evolutionary search algorithm to include internal optimization, selection and construction of the search model are now beginning to be investigated.
60 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...For the test case shown in Fig....
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...Structure factors for each solution are calculated rapidly during the course of the optimization by pre-calculating the molecular transform of the search model and applying the rotations and translations in reciprocal space (Lattman & Love, 1970; Huber & Schneider, 1985; Castellano et al., 1992)....
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TL;DR: The novel feature of the RSRef2000 software is the combination of simulated-annealing optimization with local real-space refinement, allowing several local minima to be explored quickly and automatically within the context of interactive model building.
Abstract: Methods have been developed that further automate the building of macromolecular structures into electron-density maps. The software supports molecular-dynamics real-space refinement of an atomic model to local regions of a map within the context of a popular molecular-modeling program, O [Jones et al. (1991), Acta Cryst. A47, 110–119]. It is implemented as a module to the CNS refinement package [Brunger et al. (1998), Acta Cryst. D54, 905–921], controlled by a graphical user interface and commands executed directly through the molecular-graphics package. The method is illustrated with examples of the building and rebuilding of protein and nucleic acid models in which laborious manual adjustments are avoided. The resulting models show improved convergence during subsequent reciprocal-space refinement. The novel feature of the RSRef2000 software is the combination of simulated-annealing optimization with local real-space refinement, allowing several local minima to be explored quickly and automatically within the context of interactive model building.
60 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...Our own methods (Blanc & Chapman, 1997) have focused on obtaining the very best ®t of model to map....
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...Our ®rst implementation (Blanc & Chapman, 1997) was as a module for TNT (Tronrud et al., 1987), whose gradient-descent optimizer limited the search to a single local minimum....
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TL;DR: An automatic data-collection system has been implemented and installed on seven insertion-device beamlines and a bending-magnet beamline at the ESRF as part of the SPINE (Structural Proteomics In Europe) development of an automated structure-determination pipeline.
Abstract: An automatic data-collection system has been implemented and installed on seven insertion-device beamlines and a bending-magnet beamline at the ESRF (European Synchrotron Radiation Facility) as part of the SPINE (Structural Proteomics In Europe) development of an automated structure-determination pipeline. The system allows remote interaction with beamline-control systems and automatic sample mounting, alignment, characterization, data collection and processing. Reports of all actions taken are available for inspection via database modules and web services.
59 citations
Cites background or methods from "J. Appl. Cryst.の発刊に際して"
...Simple loop centring is robust and fast, but determination of a crystal’s position within a loop is more difficult (Andrey et al., 2004)....
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...D62, 1162–1169 Acta Crystallographica Section D Biological Crystallography ISSN 0907-4449 High-throughput sample handling and data collection at synchrotrons: embedding the ESRF into the high-throughput gene-to-structure pipeline...
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...If many samples are to be screened, a robotic sample changer (Snell et al., 2004; Cohen et al., 2002; Ohana et al., 2004) and software capable of automatic alignment of samples to the X-ray beam (Andrey et al., 2004) are essential and development of these has been funded by SPINE....
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TL;DR: In this paper, the texture analysis was performed both with the Williams-Imhof-Matthies-Vinel (WIMV) method and the harmonic method, implemented in the program package MAUD.
Abstract: Orientation distributions of garnet and omphacite in eclogite from the ultra-high pressure Dabie Shan belt in east-central China were determined from neutron diffraction data by the Rietveld method. Diffraction spectra were recorded in 16 sample orientations with seven detectors, with a kappa-geometry texture goniometer at the time-of-flight (TOF) neutron facility at the Intense Pulsed Neutron Source (IPNS). The textures of the two minerals were extracted simultaneously from 16 × 7 = 112 diffraction spectra, covering a large portion of the pole figure. The texture analysis was performed both with the Williams–Imhof–Matthies–Vinel (WIMV) method and the harmonic method, implemented in the program package MAUD. The incomplete pole-figure coverage introduced artificial oscillations in the case of the harmonic method. The discrete WIMV method produced better results, which illustrate a more or less random orientation distribution for cubic garnet. Apparently elongated grains turned out to be layers of randomly oriented crystals. Monoclinic omphacite displays a sharp texture, with [001] parallel to the lineation direction. The texture data obtained by neutron diffraction were verified with EBSP (electron backscatter pattern) measurements.
59 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...Rietveld (1969) proposed the use of continuous powder patterns and his method is implemented in several software packages [e.g. DBWS (Wiles & Young, 1981), GSAS (Larson & Von Dreele, 1986) and Fullprof (Rodriguez-Carvajal et al., 1991)]....
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TL;DR: A modified multislice method has been developed for calculations of Convergent Beam Electron Diffraction (CBED) patterns and has been proofed by comparison to Bloch-wave calculations, leading to the new understanding of CBED patterns formation.
59 citations
Cites methods from "J. Appl. Cryst.の発刊に際して"
...The validity of the method for HOLZ- and Kikuchi-line calculations has been proofed by comparison to Bloch-wave calculations....
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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.
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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.
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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'.
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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.
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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