Low-resolution Data (low-resolution + data)

Distribution by Scientific Domains


Selected Abstracts


EXPO2009: structure solution by powder data in direct and reciprocal space

JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 6 2009
Angela Altomare
The program EXPO2009 is the evolution of EXPO2004 [Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni & Rizzi (2004). J. Appl. Cryst. 37, 1025,1028]. EXPO2009 performs all the steps of ab initio structure solution by powder data: indexing, space-group determination, estimation of the reflection integrated intensities, structure solution by direct/Patterson methods and/or by a direct-space/hybrid approach, and model refinement by the Rietveld technique. New procedures have been introduced in EXPO2009 for enhancing the structure solution process, particularly in the case of low-resolution data and/or organic compounds, when traditional approaches like direct methods may fail. The EXPO2009 graphical interface has been optimized and made very user friendly. [source]


Bulk-solvent correction for fast translation search in molecular replacement: service programs for AMoRe and CNS

JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2003
Andrei Fokine
A new software package, BULK, was developed to allow fast and easy use of low-resolution data for the translation problem in molecular replacement. When the search model is relatively complete but not precise, or when its orientation is imprecisely determined, low-resolution data contribute very favourably to the solution of the translation-search problem. BULK comprises a specially developed program and a set of procedures complementary to the program AMoRe, as well as an input file for the CNS suite. [source]


The statistics of the highest E value

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2007
Grzegorz Chojnowski
In a previous publication, the Gumbel,Fisher,Tippett (GFT) extreme-value analysis has been applied to investigate the statistics of the intensity of the strongest reflection in a thin resolution shell. Here, a similar approach is applied to study the distribution, expectation value and standard deviation of the highest normalized structure-factor amplitude (E value). As before, acentric and centric reflections are treated separately, a random arrangement of scattering atoms is assumed, and E -value correlations are neglected. Under these assumptions, it is deduced that the highest E value is GFT distributed to a good approximation. Moreover, it is shown that the root of the expectation value of the highest `normalized' intensity is not only an upper limit for the expectation value of the highest E value but also a very good estimate. Qualitatively, this can be attributed to the sharpness of the distribution of the highest E value. Although the formulas were derived with various simplifying assumptions and approximations, they turn out to be useful also for real small-molecule and protein crystal structures, for both thin and thick resolution shells. The only limitation is that low-resolution data (below 2.5,Å) have to be excluded from the analysis. These results have implications for the identification of outliers in experimental diffraction data. [source]


On the use of low-resolution data for translation search in molecular replacement

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2002
Andrei Fokine
Low-resolution reflections (approximately 15,Å and lower) are very useful for the translation search in molecular replacement because they are less sensitive to model errors compared with the traditionally used reflections of resolution 4,10,Å. At low resolution, however, the contribution from the bulk solvent is quite significant and corresponding structure factors calculated from a macromolecular model cannot be compared with experimental values if this contribution is neglected. The proposed method provides a way of fast translation searches where low-resolution reflections are taken into account. Test calculations using several experimental data sets show a dramatic improvement in the signal after the bulk-solvent correction and low-resolution reflections were included in the calculation; this improvement allowed unambiguous identification of the solution. [source]


A parsimonious crop-water productivity index: an application to Brazil

AREA, Issue 1 2009
Marco P Maneta
Reducing poverty in rural areas of developing countries requires sustained and sustainable increases in agricultural water productivity. However, aside from traditional measures of precipitation, little is known about water available to farmers or how productively they use it. We present a crop-water productivity index (a ratio of the value of annual crop production to a dimensionless potential water availability index) for large water basins using readily available low-resolution data. The index is transferable, permits direct inter-basin comparisons, and is simple to calculate. We calculate the index for each municipality in the São Francisco river basin in Brazil. No clear patterns linking water availability and value of agricultural output are evident, even though clusters of municípios with high- and low-crop-water productivity emerge, and the former may be useful in guiding policies aimed at increasing water productivity. Finally, analyses of the effects of information uncertainty on the crop-water productivity index suggest that the returns to agricultural investments in certain places in the São Francisco river basin are more risky than others. Improvements in data quality and quantity can help refine estimates of the index and reduce their uncertainty. [source]


A smooth and differentiable bulk-solvent model for macromolecular diffraction

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2010
T. D. Fenn
Inclusion of low-resolution data in macromolecular crystallography requires a model for the bulk solvent. Previous methods have used a binary mask to accomplish this, which has proven to be very effective, but the mask is discontinuous at the solute,solvent boundary (i.e. the mask value jumps from zero to one) and is not differentiable with respect to atomic parameters. Here, two algorithms are introduced for computing bulk-solvent models using either a polynomial switch or a smoothly thresholded product of Gaussians, and both models are shown to be efficient and differentiable with respect to atomic coordinates. These alternative bulk-solvent models offer algorithmic improvements, while showing similar agreement of the model with the observed amplitudes relative to the binary model as monitored using R, Rfree and differences between experimental and model phases. As with the standard solvent models, the alternative models improve the agreement primarily with lower resolution (>6,Å) data versus no bulk solvent. The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography. [source]


Direct methods and protein crystallography at low resolution

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2000
Christopher J. Gilmore
The tools of modern direct methods are examined and their limitations for solving protein structures discussed. Direct methods need atomic resolution data (1.1,1.2,Å) for structures of around 1000 atoms if no heavy atom is present. For low-resolution data, alternative approaches are necessary and these include maximum entropy, symbolic addition, Sayre's equation, group scattering factors and electron microscopy. [source]