Calibration of spiral-readout image-plate detectors

1999 ◽  
Vol 32 (1) ◽  
pp. 65-70 ◽  
Author(s):  
Mark A. White ◽  
Stanley J. Watowich ◽  
Robert O. Fox
Keyword(s):  
Diffraction Data ◽  
Diagnostic Tool ◽  
Improved Method ◽  
Calibration Table ◽  
Image Plate ◽  
Typical Data ◽  
Additional Equipment ◽  
Beam Center ◽  
Data Collections ◽  
Spiral Readout

An improved method for intensity-uniformity calibration of diffraction data collected on spiral-readout image-plate (IP) systems is described. This technique is applicable to all types of spiral-readout IP detectors. The procedure utilizes an attenuated direct-beam scan of the IP to generate a radial-sensitivity calibration table. Exposure and scanning of the calibration frame are done on the same time scale as typical data collections, and require no additional equipment. Specific examples are presented for use with Mac Science DIP2000 systems. The new radial calibration is shown to reduce significantly structure-basedRfactors. The improved radial calibration is also shown to lowerRmergewhen the IP is offset from the beam center. In addition to improving data quality and statistics, this method provides a quick and simple diagnostic tool to monitor changes in the sensitivity of the IP detector as a function of age.

Matrix-free integration of image-plate diffraction data

2005 ◽  
Vol 38 (2) ◽  
pp. 280-290 ◽  
Author(s):  
Ralf Müller ◽  
Georg Roth
Keyword(s):  
Coordinate System ◽  
Single Crystals ◽  
Diffraction Data ◽  
Diffuse Scattering ◽  
Area Detector ◽  
Image Plate ◽  
Data Collections ◽  
Ccd Detectors ◽  
Matrix Free ◽  
Complete Program

Matrix-free integration of area-detector diffraction data is developed to interpret data collections from single crystals, twinned or multi-phased crystals as well as quasicrystals. A pixel-background method based on the algorithm described by Bolotovsky, White, Darovsky & Coppens [J. Appl. Cryst.(1995),28, 86–95] is employed. The method is modified by using an azimuthal coordinate system and distinguishes reliably between significant scattering intensities and background intensities. Very broad intensity distributions frome.g.powder rings can be determined and reflections superimposed by diffuse scattering can be integrated reliably. A complete program suite to process area-detector data, both from image-plate and CCD detectors, is presented. The program uses both matrix-free as well as matrix-based integration. The program is tested on single-crystal and twinned-crystal diffraction data.

The direct determination of X-ray diffraction data from specific depths

2005 ◽  
Vol 20 (3) ◽  
pp. 233-240
Author(s):  
A. Broadhurst ◽  
K. D. Rogers ◽  
D. W. Lane ◽  
T. W. Lowe
Keyword(s):  
Diffraction Data ◽  
Direct Method ◽  
Direct Determination ◽  
Simulated Data ◽  
X Ray Diffraction ◽  
Linear Absorption ◽  
X Ray ◽  
Measured Angle ◽  
Data Collections

A direct method for determining powder diffraction data from a range of depths is described, where the linear absorption coefficient may vary with depth. A series of traditional data collections with varying angles of incidence are required, and the X-ray diffraction data arising from specific depths will be calculated by the transformation of these measured, angle-dependent spectra. These may then be analysed using any conventional method in order to gain information about characteristics of the sample in question at specific depths. Regularisation techniques have been used to solve the governing Fredholm integral equation to determine the depth-dependent diffractograms. The method has been validated by the use of simulated data having known model profiles, and has also been applied to experimental data from polycrystalline thin film samples.

scholarly journals Scaling diffraction data in the DIALS software package: algorithms and new approaches for multi-crystal scaling

2020 ◽  
Vol 76 (4) ◽  
pp. 385-399 ◽  
Author(s):  
James Beilsten-Edmands ◽  
Graeme Winter ◽  
Richard Gildea ◽  
James Parkhurst ◽  
David Waterman ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Global Radiation ◽  
Point Group ◽  
Group Symmetry ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Data Set ◽  
Data Collections ◽  
Free Set ◽  
Scaling Algorithms

In processing X-ray diffraction data, the intensities obtained from integration of the diffraction images must be corrected for experimental effects in order to place all intensities on a common scale both within and between data collections. Scaling corrects for effects such as changes in sample illumination, absorption and, to some extent, global radiation damage that cause the measured intensities of symmetry-equivalent observations to differ throughout a data set. This necessarily requires a prior evaluation of the point-group symmetry of the crystal. This paper describes and evaluates the scaling algorithms implemented within the DIALS data-processing package and demonstrates the effectiveness and key features of the implementation on example macromolecular crystallographic rotation data. In particular, the scaling algorithms enable new workflows for the scaling of multi-crystal or multi-sweep data sets, providing the analysis required to support current trends towards collecting data from ever-smaller samples. In addition, the implementation of a free-set validation method is discussed, which allows the quantification of the suitability of scaling-model and algorithm choices.

Improvement of deconvolution–convolution treatment of axial-divergence aberration in Bragg–Brentano geometry

2018 ◽  
Vol 33 (2) ◽  
pp. 121-133 ◽  
Author(s):  
Takashi Ida ◽  
Shoki Ono ◽  
Daiki Hattan ◽  
Takehiro Yoshida ◽  
Yoshinobu Takatsu ◽  
...  
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Peak Shift ◽  
Powder Diffraction Data ◽  
Shape Parameters ◽  
Improved Method ◽  
One Dimensional ◽  
Diffraction Angle ◽  
Cumulant Analysis ◽  
Best Fit

An improved method to correct observed shift and asymmetric deformation of diffraction peak profile caused by the axial-divergence aberration in Bragg–Brentano geometry is proposed. The method is based on deconvolution–convolution treatment applying scale transform of abscissa, Fourier transform, and cumulant analysis of an analytical model for the axial-divergence aberration. The method has been applied to the powder diffraction data of a standard LaB6 powder (NIST SRM660a) sample, collected with a one-dimensional Si strip detector. The locations, widths and shape of the peaks in the deconvolved–convolved powder diffraction data have been analyzed. The finally obtained whole powder diffraction pattern ranging from 10° to 145° in diffraction angle has been simulated by the Pawley method applying a symmetric Pearson VII peak profile model to each peak with ten background, two peak-shift, three line-width, and two peak-shape parameters, and the Rp value of the best fit has been estimated at 4.4%.

Crystal Structure Determination of Glycerol-Containing Lipids from Electron Diffraction Data. Use of Analog Compounds Based upon Configurational Isomers of Cyclopentane-1, 2, 3-TRIOL

1977 ◽  
Vol 35 ◽  
pp. 24-25
Author(s):  
Douglas L. Dorset ◽  
Anthony J. Hancock
Keyword(s):  
Crystal Structure ◽  
Electron Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Crystal Surface ◽  
Coherent Scattering ◽  
Crystal Structure Determination ◽  
Electron Diffraction Data ◽  
Polar Group ◽  
Axis Orientation

Lipids containing long polymethylene chains were among the first compounds subjected to electron diffraction structure analysis. It was only recently realized, however, that various distortions of thin lipid microcrystal plates, e.g. bends, polar group and methyl end plane disorders, etc. (1-3), restrict coherent scattering to the methylene subcell alone, particularly if undistorted molecular layers have well-defined end planes. Thus, ab initio crystal structure determination on a given single uncharacterized natural lipid using electron diffraction data can only hope to identify the subcell packing and the chain axis orientation with respect to the crystal surface. In lipids based on glycerol, for example, conformations of long chains and polar groups about the C-C bonds of this moiety still would remain unknown.One possible means of surmounting this difficulty is to investigate structural analogs of the material of interest in conjunction with the natural compound itself. Suitable analogs to the glycerol lipids are compounds based on the three configurational isomers of cyclopentane-1,2,3-triol shown in Fig. 1, in which three rotameric forms of the natural glycerol derivatives are fixed by the ring structure (4-7).

Toward an alignment of the actin molecule within the actin filament

1983 ◽  
Vol 41 ◽  
pp. 450-451
Author(s):  
P.R. Smith ◽  
W.E. Fowler ◽  
U. Aebi
Keyword(s):  
Actin Filament ◽  
Diffraction Data ◽  
Quantitative Estimate ◽  
Molecular Model ◽  
Quantitative Comparison ◽  
Regulatory Proteins ◽  
Essential Information ◽  
X Ray ◽  
Maximum Resolution ◽  
Lack Of Information

An understanding of the specific interactions of actin with regulatory proteins has been limited by the lack of information about the structure of the actin filament. Molecular actin has been studied in actin-DNase I complexes by single crystal X-ray analysis, to a resolution of about 0.6nm, and in the electron microscope where two dimensional actin sheets have been reconstructed to a maximum resolution of 1.5nm. While these studies have shown something of the structure of individual actin molecules, essential information about the orientation of actin in the filament is still unavailable.The work of Egelman & DeRosier has, however, suggested a method which could be used to provide an initial quantitative estimate of the orientation of actin within the filament. This method involves the quantitative comparison of computed diffraction data from single actin filaments with diffraction data derived from synthetic filaments constructed using the molecular model of actin as a building block. Their preliminary work was conducted using a model consisting of two juxtaposed spheres of equal size.

Automatic measurement of SAED patterns from asbestos minerals

1988 ◽  
Vol 46 ◽  
pp. 846-847
Author(s):  
J. C. Russ ◽  
T. Taguchi ◽  
P. M. Peters ◽  
E. Chatfield ◽  
J. C. Russ ◽  
...  
Keyword(s):  
Diffraction Pattern ◽  
High Precision ◽  
Diffraction Data ◽  
Automatic Measurement ◽  
Automatic Method ◽  
Important Method ◽  
X Ray ◽  
Integrated Intensity ◽  
Asbestiform Minerals ◽  
True Center

Conventional SAD patterns as obtained in the TEM present difficulties for identification of materials such as asbestiform minerals, although diffraction data is considered to be an important method for making this purpose. The preferred orientation of the fibers and the spotty patterns that are obtained do not readily lend themselves to measurement of the integrated intensity values for each d-spacing, and even the d-spacings may be hard to determine precisely because the true center location for the broken rings requires estimation. We have implemented an automatic method for diffraction pattern measurement to overcome these problems. It automatically locates the center of patterns with high precision, measures the radius of each ring of spots in the pattern, and integrates the density of spots in that ring. The resulting spectrum of intensity vs. radius is then used just as a conventional X-ray diffractometer scan would be, to locate peaks and produce a list of d,I values suitable for search/match comparison to known or expected phases.

An Improved Method for the Preparation and TEM Examination of Sharp Pointed Tips used in APFIM and STM

1990 ◽  
Vol 48 (2) ◽  
pp. 102-103
Author(s):  
E.A. Fischione ◽  
P.E. Fischione ◽  
J.J. Haugh ◽  
M.G. Burke
Keyword(s):  
Atom Probe ◽  
Preparation Process ◽  
Improved Method ◽  
Ion Milling ◽  
Polishing Process ◽  
Probe Field ◽  
Scanning Tunnelling ◽  
Stm Tips ◽  
Tunnelling Microscopy ◽  
Ion Microscopy

A common requirement for both Atom Probe Field-Ion Microscopy (APFIM) and Scanning Tunnelling Microscopy (STM) is a sharp pointed tip for use as either the specimen (APFIM) or the probe (STM). Traditionally, tips have been prepared by either chemical or electropolishing techniques. Recently, ion-milling has been successfully employed in the production of APFIM tips [1]. Conventional electropolishing techniques are applicable to a wide variety of metals, but generally require careful manual adjustments during the polishing process and may also be time-consuming. In order to reduce the time and effort involved in the preparation process, a compact, self-contained polishing unit has been developed. This system is based upon the conventional two-stage electropolishing technique in which the specimen/tip blank is first locally thinned or “necked”, and subsequently electropolished until separation occurs.[2,3] The result of this process is the production of two APFIM or STM tips. A mechanized polishing unit that provides these functions while automatically maintaining alignment has been designed and developed.

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