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Data Resolution (data + resolution)
Selected AbstractsAdvances in the free lunch methodJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 5 2007Rocco Caliandro The most critical limit of macromolecular crystallography, the experimental data resolution, is partially `tricked' by the `free lunch method' (non-measured reflection extrapolation). The best electron density map available when only observed data are used may be employed to extrapolate moduli and phases of unobserved reflections behind and beyond the experimental resolution limit. The method is able to reduce the mean phase error of the observed reflections and to produce a more interpretable (in terms of a molecular model) electron density map. The main features of the free lunch method have been studied and its performance has been enhanced; it is beneficial even if data resolution is about 2,Å. Furthermore, the technique has been parameterized so that it may be routinely used by other phasing programs. [source] TO DIVE OR NOT TO DIVE: SCUBA VERSUS ROV SAMPLING OF MACROALGAE AT 30M DEPTHJOURNAL OF PHYCOLOGY, Issue 2001Article first published online: 24 SEP 200 Spalding, H. L. Moss Landing Marine Laboratories, 8272 Moss Landing, Rd., Moss Landing, CA 95039 USA Remotely Operated Vehicles (ROVs) and enriched air Nitrox SCUBA diving have recently become available to researchers for studying the deep-water environment. Each use a different technique for collecting macroalgal abundance data: ROVs use collections and high-resolution digital video which can be quantified using an integrative laser and computer imagery program (high tech), while divers often count the densities of individuals and use a point contact method for sampling percent (%) cover in situ (low tech). While the types of data collected by both techniques are the same, the effects of the different sampling methods on data resolution are unknown. As part of a larger study on deep-water macroalgae in central California, I compared the abundance of common macroalgae (% cover of macroalgal groups and individuals/m2) collected by divers and the ROV Ventana at a depth of 30m at 3 locations in central California. Generally, there were no significant differences between diver and ROV data in the % cover of coralline Rhodophyta, non-coralline Rhodophyta, and Pleurophycus gardneri/m2. The use of a laser-calibrated computer imagery program and an ROV with user-controlled lighting greatly decreased lab analysis time, and a method for sampling macroalgal layers with the ROV was developed. Thus, ROVs with high-resolution digital video and supplemental macroalgal collections can be used to quantify deep-water algae as accurately as in situ divers, but without the limited dive time, depth limits, and physical demands of the latter. [source] GIS-based rapid assessment of erosion risk in a small catchment in the wet/dry tropics of AustraliaLAND DEGRADATION AND DEVELOPMENT, Issue 5 2001G. Boggs Abstract Assessing the impact of various land uses on catchment erosion processes commonly requires in-depth research, monitoring and field data collection, as well as the implementation of sophisticated modelling techniques. This paper describes the evaluation of a geographic information system (GIS)-based rapid erosion assessment method, which allows the user to quickly acquire and evaluate existing data to assist in the planning of more detailed monitoring and modelling programmes. The rapid erosion assessment method is based on a simplified version of the revised universal soil loss equation (RUSLE), and allows the rapid parameterization of the model from widely available land unit and elevation datasets. The rapid erosion assessment method is evaluated through the investigation of the effects of elevation data resolution on erosion predictions and field data validation. The use of raster digital elevation model (DEM)-derived data, as opposed to vector land unit relief data, was found to greatly improve the validity of the rapid erosion assessment method. Field validation of the approach, involving the comparison of predicted soil loss ratios with adjusted in-stream sediment yields on a subcatchment basis, indicated that with decreasing data resolution, the results are increasingly overestimated for larger catchments and underestimated for smaller catchments. However, the rapid erosion assessment method proved to be a valuable tool that is highly useful as an initial step in the planning of more detailed erosion assessments. Copyright © 2001 Commonwealth of Australia. [source] The invariom model and its application: refinement of d,l -serine at different temperatures and resolutionACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2005B. Dittrich Three X-ray data sets of the same d,l -serine crystal were measured at temperatures of 298, 100 and 20,K. These data were then evaluated using invarioms and the Hansen & Coppens aspherical-atom model. Multipole populations for invarioms, which are pseudoatoms that remain approximately invariant in an intermolecular transfer, were theoretically predicted using different density functional theorem (DFT) basis sets. The invariom parameters were kept fixed and positional and thermal parameters were refined to compare the fitting against the multi-temperature data at different resolutions. The deconvolution of thermal motion and electron density with respect to data resolution was studied by application of the Hirshfeld test. Above a resolution of sin,/,,,,0.55,Å,1, or d,,,0.9,Å, this test was fulfilled. When the Hirshfeld test is fulfilled, a successful modeling of the aspherical electron density with invarioms is achieved, which was proven by Fourier methods. Molecular geometry improves, especially for H atoms, when using the invariom method compared to the independent-atom model, as a comparison with neutron data shows. Based on this example, the general applicability of the invariom concept to organic molecules is proven and the aspherical density modeling of a larger biomacromolecule is within reach. [source] An evolutionary computational approach to the phase problem in macromolecular X-ray crystallographyACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2001Gordon Webster The ab initio computation of the molecular envelopes of two proteins exclusively from their corresponding diffraction amplitudes demonstrates that an efficient and inherently parallel evolutionary search algorithm can assist in the direct phasing of macromolecules for which almost no a priori structural information is available. The applicability of this evolutionary computational approach is general and should not be limited to the examples described nor to extremes of data resolution, symmetry or structural size. [source] Accurate charge density of the tripeptide Ala-Pro-Ala with the maximum entropy method (MEM): influence of data resolutionACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2007Andreas Hofmann The accurate electron density of Ala-Pro-Ala is determined by the maximum entropy method (MEM), employing the same reflection data measured at 100,K which was used for a multipole refinement by Kalinowski et al. [(2007), Acta Cryst. Accepted for publication]. Properties of the electron density are compared with the corresponding properties of the static electron density from the multipole model and to the dynamic MEM electron density of trialanine at 20,K. It is thus shown that the increased thermal smearing at 100,K leads to lower electron densities in the bond critical points and atomic charges closer to zero for Ala-Pro-Ala than has been obtained for trialanine at 20,K. The influence of the resolution of the data is investigated by a series of MEM calculations. Atomic charges and atomic volumes are found not to depend on the resolution, but the charge density in the BCPs decreases with decreasing resolution of the dataset. The origin of this dependence is found to lie mostly in the more accurate estimate of the atomic displacement parameters (ADPs) for the higher-resolution datasets. If these effects are taken into account, meaningful information on chemical bonding can be obtained with data at a resolution better than dmin = 0.63,Å. Alternatively, low-resolution X-ray diffraction data can be used in accurate electron-density studies by the MEM, if another source of accurate values of the ADPs is available, e.g. from refinements with multipole parameters from a database of transferable multipole parameters. [source] MAD phasing: choosing the most informative wavelength combinationACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2004Maria Cristina Burla Two algorithms are described for limiting data resolution and for predicting the most informative wavelength combinations in MAD techniques. Both have been successfully tested using experimental data from a large set of test structures. [source] About the efficiency of the early FOMs in ab initio protein phasingJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 5 2004Maria C. Burla All ab initio techniques for solving protein crystal structures use multisolution approaches. Several figures of merit that are found in the literature are efficient in the last steps of the phasing process, when some trials converge to the correct solution with a relatively small average phase error. Early figures of merit are much more critical; they should be able to recognize useful trials when the phase error is still large, and their efficiency determines the efficiency of the program. In the present work, a wide variety of known figures of merit at atomic and quasi-atomic (,1.4,Å) resolution have been tested; new figures have also been devised and tested. Their application to a large set of test structures allows the study of their properties at different data resolutions and the selection of the most efficient figures within the SIR2003-N framework. [source] Combining experimental data for structure determination of flexible multimeric macromolecules by molecular replacementACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2006Stefano Trapani A major effort has been made by the structural biology community to develop user-friendly software for the use of biologists. However, structural projects become more and more challenging and their solution often relies on a combination of information from various sources. Here, it is described how X-ray data, normal-mode analysis (NMA) and electron-microscopy (EM) data can be successfully combined in order to obtain a molecular-replacement (MR) solution for crystal structures containing multimeric molecules. NMA is used to simulate computationally the inherent internal flexibility of the monomer and thus enhance, together with the crystal noncrystallographic symmetry (NCS), the MR capabilities. NCS is also used to obtain a reliable EM reconstruction, which is then employed as a filter to construct oligomers starting from monomers. The feasibility of the direct use of EM reconstructions as a template for MR when the X-ray and EM data resolutions overlap is also discussed. [source] | ||||||||||