scholarly journals Aspects of direct phasing in femtosecond nanocrystallography

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130498 ◽  
Author(s):  
Rick P. Millane ◽  
Joe P. J. Chen
Keyword(s):  
Free Electron Laser ◽  
Phase Retrieval ◽  
Laser Diffraction ◽  
Intensity Data ◽  
Noise Levels ◽  
Signal To Noise ◽  
X Ray ◽  
Unit Cells ◽  
Diffraction Patterns ◽  
Selection Of

X-ray free-electron laser diffraction patterns from protein nanocrystals provide information on the diffracted amplitudes between the Bragg reflections, offering the possibility of direct phase retrieval without the use of ancillary experimental data. Proposals for implementing direct phase retrieval are reviewed. These approaches are limited by the signal-to-noise levels in the data and the presence of different and incomplete unit cells in the nanocrystals. The effects of low signal to noise can be ameliorated by appropriate selection of the intensity data samples that are used. The effects of incomplete unit cells may be small in some cases, and a unique solution is likely if there are four or fewer molecular orientations in the unit cell.

Direct phasing in femtosecond nanocrystallography. II. Phase retrieval

2014 ◽  
Vol 70 (2) ◽  
pp. 154-161 ◽  
Author(s):  
Joe P. J. Chen ◽  
John C. H. Spence ◽  
Rick P. Millane
Keyword(s):  
Free Electron Laser ◽  
Phase Retrieval ◽  
Laser Diffraction ◽  
Selection Strategy ◽  
Noise Levels ◽  
Acta Cryst ◽  
X Ray ◽  
Retrieval Algorithms ◽  
Simulation Results ◽  
Diffraction Patterns

X-ray free-electron laser diffraction patterns from protein nanocrystals provide information on the diffracted amplitudes between the Bragg reflections, offering the possibility of direct phase retrieval without the use of ancillary experimental diffraction data [Spenceet al.(2011).Opt. Express,19, 2866–2873]. The estimated continuous transform is highly noisy however [Chenet al.(2014).Acta Cryst.A70, 143–153]. This second of a series of two papers describes a data-selection strategy to ameliorate the effects of the high noise levels and the subsequent use of iterative phase-retrieval algorithms to reconstruct the electron density. Simulation results show that employing such a strategy increases the noise levels that can be tolerated.

scholarly journals FELIX: an algorithm for indexing multiple crystallites in X-ray free-electron laser snapshot diffraction images

2017 ◽  
Vol 50 (4) ◽  
pp. 1075-1083 ◽  
Author(s):  
Kenneth R. Beyerlein ◽  
Thomas A. White ◽  
Oleksandr Yefanov ◽  
Cornelius Gati ◽  
Ivan G. Kazantsev ◽  
...  
Keyword(s):  
Free Electron Laser ◽  
Signal To Noise Ratio ◽  
X Ray Diffraction ◽  
Signal To Noise ◽  
Monoclinic Crystal ◽  
Slight Tendency ◽  
X Ray ◽  
Serial Crystallography ◽  
Diffraction Patterns ◽  
Novel Algorithm

A novel algorithm for indexing multiple crystals in snapshot X-ray diffraction images, especially suited for serial crystallography data, is presented. The algorithm, FELIX, utilizes a generalized parametrization of the Rodrigues–Frank space, in which all crystal systems can be represented without singularities. The new algorithm is shown to be capable of indexing more than ten crystals per image in simulations of cubic, tetragonal and monoclinic crystal diffraction patterns. It is also used to index an experimental serial crystallography dataset from lysozyme microcrystals. The increased number of indexed crystals is shown to result in a better signal-to-noise ratio, and fewer images are needed to achieve the same data quality as when indexing one crystal per image. The relative orientations between the multiple crystals indexed in an image show a slight tendency of the lysozme microcrystals to adhere on (\overline 110) facets.

scholarly journals Phasing coherently illuminated nanocrystals bounded by partial unit cells

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130331 ◽  
Author(s):  
Richard A. Kirian ◽  
Richard J. Bean ◽  
Kenneth R. Beyerlein ◽  
Oleksandr M. Yefanov ◽  
Thomas A. White ◽  
...  
Keyword(s):  
Approximate Solution ◽  
Diffraction Data ◽  
Free Electron ◽  
Free Electron Laser ◽  
A Priori ◽  
Iterative Algorithms ◽  
Phase Problem ◽  
X Ray ◽  
Unit Cells ◽  
Diffraction Patterns

With the use of highly coherent femtosecond X-ray pulses from a free-electron laser, it is possible to record protein nanocrystal diffraction patterns with far more information than is present in conventional crystallographic diffraction data. It has been suggested that diffraction phases may be retrieved from such data via iterative algorithms, without the use of a priori information and without restrictions on resolution. Here, we investigate the extension of this approach to nanocrystals with edge terminations that produce partial unit cells, and hence cannot be described by a common repeating unit cell. In this situation, the phase problem described in previous work must be reformulated. We demonstrate an approximate solution to this phase problem for crystals with random edge terminations.

scholarly journals Comparison of EMC and CM methods for orienting diffraction images in single-particle imaging experiments

IUCrJ ◽  
2021 ◽  
Vol 8 (6) ◽  
Author(s):  
Miklós Tegze ◽  
Gábor Bortel
Keyword(s):  
Intensity Distribution ◽  
Single Particle ◽  
Free Electron ◽  
Free Electron Laser ◽  
Biological Molecules ◽  
Crucial Step ◽  
X Ray ◽  
Diffraction Patterns ◽  
Particle Imaging ◽  
Single Particle Imaging

In single-particle imaging (SPI) experiments, diffraction patterns of identical particles are recorded. The particles are injected into the X-ray free-electron laser (XFEL) beam in random orientations. The crucial step of the data processing of SPI is finding the orientations of the recorded diffraction patterns in reciprocal space and reconstructing the 3D intensity distribution. Here, two orientation methods are compared: the expansion maximization compression (EMC) algorithm and the correlation maximization (CM) algorithm. To investigate the efficiency, reliability and accuracy of the methods at various XFEL pulse fluences, simulated diffraction patterns of biological molecules are used.

scholarly journals Solidified Fillings of Nanopores

2005 ◽  
Vol 876 ◽  
Author(s):  
Patrick Huber ◽  
Klaus Knorr
Keyword(s):  
Pore Diameter ◽  
Stacking Faults ◽  
Pore Geometry ◽  
X Ray Diffraction ◽  
X Ray ◽  
Medium Length ◽  
Close Packed Structure ◽  
Packed Structure ◽  
Diffraction Patterns ◽  
Selection Of

AbstractWe present a selection of x-ray diffraction patterns of spherical (He, Ar), dumbbell- (N2, CO), and chain-like molecules (n-C9H20, n-C19H40) solidified in nanopores of silica glass (mean pore diameter 7nm). These patterns allow us to demonstrate how key principles governing crystallization have to be adapted in order to accomplish solidification in restricted geometries. 4He, Ar, and the spherical close packed phases of CO and N2 adjust to the pore geometry by introducing a sizeable amount of stacking faults. For the pore solidified, medium-length chainlike n-C19H40 we observe a close packed structure without lamellar ordering, whereas for the short-chain C9H20 the layering principle survives, albeit in a modified fashion compared to the bulk phase.

Diffracted Beam Monochromators for Powder Diffractometry

1970 ◽  
Vol 14 ◽  
pp. 38-56
Author(s):  
E. M. Proctor ◽  
T. C. Furnas ◽  
W. F. Loranger
Keyword(s):  
Preferred Orientation ◽  
Signal To Noise ◽  
X Ray ◽  
Direct Beam ◽  
Vertical Divergence ◽  
Oriented Samples ◽  
Efficiency And Effectiveness ◽  
Slit System ◽  
Bent Crystals ◽  
Selection Of

AbstractThe efficiency and effectiveness of diffracted beam x-ray monochromators used in powder diffractometry have been described in so many ways that much confusion exists regarding their true performance. Although significant improvements in signal to noise ratios are readily achievable, and they offer a solution to the sample fluorescence problem, it is not without sacrifice to total intensity or achievable resolution or both. This paper discusses and describes a series of comparisons between filtered direct beam, LiF and graphite monochromators.These comparisons include the considerations necessary for the appropriate selection of diffracted beam slit system, the effect of vertical divergence as a function of two theta for singly bent crystals, the effects of a non-uniformity of contribution over the length of the crystal, and the geometry necessary for the singly bent and doubly bent crystals. The total intensity and the resolution of LiF and graphite are discussed, in particular, it is noted that the performance of monochromators with randomly oriented samples is quite different than their performance with samples showing preferred orientation or grain effects.A new diffracted beam monochromator based on the Rowland focusing geometry is described.

PreDICT: a graphical user interface to the DICVOL14 indexing software program for powder diffraction data

2019 ◽  
Vol 34 (3) ◽  
pp. 233-241 ◽  
Author(s):  
Justin R. Blanton ◽  
Robert J. Papoular ◽  
Daniel Louër
Keyword(s):  
Powder Diffraction ◽  
Laboratory Data ◽  
Graphical Interface ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Moderate Number ◽  
Diffraction Patterns ◽  
User Friendly ◽  
Recent Version ◽  
Selection Of

A straightforward intuitive user-friendly compact graphical interface, PreDICT (Premier DICVOL Tool) has been developed to take full advantage of the new capabilities of the most recent version of the DICVOL14 Indexing Software. The latter, an updated version of DICVOL04, includes optimizations, e.g. for monoclinic and triclinic cases, a detailed review of the input data from the indexing solutions, cell centering tests, as well as the handling of a moderate number of impurity peaks. Among the most salient features of PreDICT, one can mention the ability (1) to use 2θ non-equistepped input 1D X-ray powder diffraction patterns as can be obtained from 2D detectors, (2) to strip laboratory data from its Kα2 contribution when present, (3) to generate 2θ equistepped output 1D X-ray powder diffraction patterns in both the “.XY” and “.GSA” formats. In addition, PreDICT allows for the following features: (1) full access to the native DICVOL14 input/output ASCII file system is retained, (2) for any selection of a DICVOL14 suggested unit cell, all predicted Bragg peaks up to a certain 2θMAX value are clearly displayed and indicated, thereby emphasizing the contribution of the unaccounted peaks (if any) to the 1D X-ray powder diffraction pattern under current investigation.

scholarly journals Factor Analysis of XRF and XRPD Data on the Example of the Rocks of the Kontozero Carbonatite Complex (NW Russia). Part I: Algorithm

Crystals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 874
Author(s):  
Ekaterina Fomina ◽  
Evgeniy Kozlov ◽  
Ayya Bazai
Keyword(s):  
Factor Analysis ◽  
Original Method ◽  
Carbonatite Complex ◽  
X Ray ◽  
Mineral Phases ◽  
Diffraction Patterns ◽  
Sample Set ◽  
Geological Research ◽  
Representative Samples ◽  
Selection Of

This paper aims to develop a principle for selecting the most informative samples for geological research from extensive collections of rock material. As a tool for this selection, we chose an original method of statistical comparison of X-ray powder diffraction (XRPD) and X-ray fluorescence (XRF) data using factor analysis (FA). A collection of carbonatites and aluminosilicate rocks from the Kontozero Devonian carbonatite paleovolcano complex (198 samples) is presented to test our technique. The factors extracted during FA were successfully mineralogically interpreted according to peak positions on the graphs of factor loadings. For the studied rock collection, this approach allowed us to identify more than 20 rock-forming minerals based only on XRPD data. We also found about ten mineral phases, the lines of which are low-intensity, and/or which overlap with more intense peaks of other minerals in the diffraction patterns. The mineralogical interpretation of the factors of such hidden minerals can be performed through electron probe microanalysis (EPMA) of the samples previously selected using FA. In this study, we report on an algorithm that facilitates the selection of the rock samples exhibiting the greatest contrast in mineral and chemical composition and which contain the entire set of mineral phases occurring in the geological object under study. From the collection of Kontozero rocks we examined, the 30 most representative samples were selected, amounting to about 15% of the initial sample set.

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