scholarly journals HiSPoD: a program for high-speed polychromatic X-ray diffraction experiments and data analysis on polycrystalline samples

2016 ◽  
Vol 23 (4) ◽  
pp. 1046-1053 ◽  
Author(s):  
Tao Sun ◽  
Kamel Fezzaa
Keyword(s):  
Diffraction Data ◽  
High Speed ◽  
Short Pulse ◽  
Frame Rate ◽  
Short Exposure ◽  
X Rays ◽  
X Ray Diffraction ◽  
Short Exposure Time ◽  
X Ray ◽  
Structure Information

A high-speed X-ray diffraction technique was recently developed at the 32-ID-B beamline of the Advanced Photon Source for studying highly dynamic, yet non-repeatable and irreversible, materials processes. In experiments, the microstructure evolution in a single material event is probed by recording a series of diffraction patterns with extremely short exposure time and high frame rate. Owing to the limited flux in a short pulse and the polychromatic nature of the incident X-rays, analysis of the diffraction data is challenging. Here,HiSPoD, a stand-alone Matlab-based software for analyzing the polychromatic X-ray diffraction data from polycrystalline samples, is described. WithHiSPoD, researchers are able to perform diffraction peak indexing, extraction of one-dimensional intensity profiles by integrating a two-dimensional diffraction pattern, and, more importantly, quantitative numerical simulations to obtain precise sample structure information.

Masquerade: removing non-sample scattering from integrated reflection intensities

2012 ◽  
Vol 45 (2) ◽  
pp. 292-298 ◽  
Author(s):  
J. A. Coome ◽  
A. E. Goeta ◽  
J. A. K. Howard ◽  
M. R. Probert
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Low Temperatures ◽  
Test Case ◽  
X Rays ◽  
Atmospheric Conditions ◽  
X Ray Diffraction ◽  
New Approach ◽  
X Ray ◽  
Internal Agreement

X-ray diffraction experiments at very low temperatures require samples to be isolated from atmospheric conditions and held under vacuum. These conditions are usually maintainedviathe use of beryllium chambers, which also scatter X-rays, causing unwanted contamination of the sample's diffraction pattern. The removal of this contamination requires novel data-collection and processing procedures to be employed. Herein a new approach is described, which utilizes the differences in origin of scattering vectors from the sample and the beryllium to eliminate non-sample scattering. The programMasqueradehas been written to remove contaminated regions of the diffraction data from the processing programs. Coupled with experiments at different detector distances, it allows for the acquisition of decontaminated data. Studies of several single crystals have shown that this approach increases data quality, highlighted by the improvement in internal agreement factor with the test case of cytidine presented herein.

scholarly journals Measurement of persistence in YAG:Ce3+scintillator with pulsed synchrotron X-rays

2011 ◽  
Vol 18 (4) ◽  
pp. 601-604 ◽  
Author(s):  
Tatsuhito Matsuo ◽  
Naoto Yagi
Keyword(s):  
High Resolution ◽  
Decay Time ◽  
Periodic Variation ◽  
Frame Rate ◽  
X Rays ◽  
X Ray Diffraction ◽  
Cmos Camera ◽  
X Ray ◽  
Space Resolution ◽  
Focused Beam

The decay time of YAG:Ce3+phosphor was studied using a CMOS camera with a frame rate of 1302000 s−1and pulsed X-rays from SPring-8. A high-resolution X-ray detector with YAG:Ce3+was used with the camera to view the focused beam from the helical undulator. Mismatch between the ring circulation time and the frame time gave rise to a periodic variation of beam intensity in successive frames. Analysis of data obtained with two bunch modes showed that the decay time of YAG:Ce3+was 60 ns. The variation of the beam positions in isolated bunches was small enough to be neglected in experiments using the focused beam. The results also show the possibility of an X-ray diffraction study at high time and space resolution.

scholarly journals Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF

2013 ◽  
Vol 46 (3) ◽  
pp. 804-810 ◽  
Author(s):  
Stéphanie Monaco ◽  
Elspeth Gordon ◽  
Matthew W. Bowler ◽  
Solange Delagenière ◽  
Matias Guijarro ◽  
...  
Keyword(s):  
Diffraction Data ◽  
High Speed ◽  
Automatic Processing ◽  
European Synchrotron Radiation Facility ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Computing Environment ◽  
X Ray ◽  
Standard Integration ◽  
Intuitive Manner

The development of automated high-intensity macromolecular crystallography (MX) beamlines at synchrotron facilities has resulted in a remarkable increase in sample throughput. Developments in X-ray detector technology now mean that complete X-ray diffraction datasets can be collected in less than one minute. Such high-speed collection, and the volumes of data that it produces, often make it difficult for even the most experienced users to cope with the deluge. However, the careful reduction of data during experimental sessions is often necessary for the success of a particular project or as an aid in decision making for subsequent experiments. Automated data reduction pipelines provide a fast and reliable alternative to user-initiated processing at the beamline. In order to provide such a pipeline for the MX user community of the European Synchrotron Radiation Facility (ESRF), a system for the rapid automatic processing of MX diffraction data from single and multiple positions on a single or multiple crystals has been developed. Standard integration and data analysis programs have been incorporated into the ESRF data collection, storage and computing environment, with the final results stored and displayed in an intuitive manner in the ISPyB (information system for protein crystallography beamlines) database, from which they are also available for download. In some cases, experimental phase information can be automatically determined from the processed data. Here, the system is described in detail.

scholarly journals Synthesis and Rietveld crystal structure refinement of mackinawite, tetragonal FeS

1995 ◽  
Vol 59 (397) ◽  
pp. 677-683 ◽  
Author(s):  
A. R. Lennie ◽  
S. A. T. Redfern ◽  
P. F. Schofield ◽  
D. J. Vaughan
Keyword(s):  
Crystal Structure ◽  
Diffraction Data ◽  
Structure Refinement ◽  
X Rays ◽  
Crystal Structure Refinement ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters

AbstractMackinawite, tetragonal FeS, has been synthesised by reacting iron with Na2S solutions. A Rietveld structure refinement of X-ray powder diffraction data, recorded using X-rays monochromated from synchrotron radiation with a wavelength of 0.6023 Å, has been performed. The structure has been refined in the tetragonal space group, P4/nmm, and has the following cell parameters: a = 3.6735(4), c = 5.0328(7) Å, V = 67.914(24) Å3. Our refinement shows that the FeS4 tetrahedron in mackinawite is almost perfectly regular, with a much smaller distortion than has been previously reported. An improved X-ray diffraction data set is provided.

TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data

2020 ◽  
Vol 76 (3) ◽  
pp. 296-306 ◽  
Author(s):  
Kunal Kumar Jha ◽  
Barbara Gruza ◽  
Prashant Kumar ◽  
Michal Leszek Chodkiewicz ◽  
Paulina Maria Dominiak
Keyword(s):  
Neutron Diffraction ◽  
Diffraction Data ◽  
Structure Refinement ◽  
X Rays ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Bond Lengths ◽  
Atom Model ◽  
User Friendly

Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X—H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X—H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (d min ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

A system for collection and on-line integration of X-ray diffraction data from a multiwire area detector

1987 ◽  
Vol 20 (3) ◽  
pp. 235-242 ◽  
Author(s):  
M. Blum ◽  
P. Metcalf ◽  
S. C. Harrison ◽  
D. C. Wiley
Keyword(s):  
Diffraction Data ◽  
High Speed ◽  
X Ray Diffraction ◽  
Quality Of Data ◽  
X Ray ◽  
Camera Control ◽  
Area Detector ◽  
C Programming ◽  
On Line ◽  
Integrated Intensities

A system for collecting and measuring X-ray diffraction data from protein crystals has been developed for a multiwire area detector. Computer programs run concurrently on two microcomputers, which collect and reduce detector data to integrated intensities. The self-contained system consists of an X-ray area detector, a rotation/oscillation camera, and two microcomputers connected by a high-speed Ethernet network. One microcomputer is dedicated to operation of the detector, control of the camera, and storage of the raw data. The second microcomputer automatically integrates the data as they are collected and allows the user to monitor the quality of data as they are processed. The integration programs are written in Fortran 77 and have been designed to be portable. Additional programs for crystal alignment, detector and camera control, and graphics are written in the C programming language. A description of the system, some characteristics of the detector, and the results of data collection are presented.

Estimation of Order Parameter and Spin Moment of Fe3Pt by White X-Ray Diffraction Method

2013 ◽  
Vol 596 ◽  
pp. 3-7
Author(s):  
Kenta Hiiragi ◽  
Masahiro Naito ◽  
Hiromi Watanabe ◽  
Hiroshi Maruyama ◽  
Masahisa Ito
Keyword(s):  
Synchrotron Radiation ◽  
Diffraction Data ◽  
Order Parameter ◽  
Diffraction Method ◽  
Superlattice Reflection ◽  
Spin Moment ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
Pt Alloy

Diffraction intensities of a single crystal of Fe3Pt alloy have been measured by using white X-rays of synchrotron radiation. The observed intensities have been compared with the calculated ones for fundamental and superlattice reflections. By normalizing the calculated intensities of fundamental reflections to the observed ones and evaluating the ratio of the observed intensity of superlattice reflection to the calculated ones, we have estimated the order parameter as 0.82±0.03. The obtained order parameter has been applied to an analysis of the X-ray magnetic diffraction data to estimate the spin moment of Fe and Pt atoms in this alloy.

scholarly journals High-resolution macromolecular crystallography at the FemtoMAX beamline with time-over-threshold photon detection

2021 ◽  
Vol 28 (1) ◽  
pp. 64-70
Author(s):  
Maja Jensen ◽  
Viktor Ahlberg Gagnér ◽  
Juan Cabello Sánchez ◽  
Åsa U. J. Bengtsson ◽  
J. Carl Ekström ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Protein Function ◽  
Short Pulse ◽  
Protein Structures ◽  
Single Photons ◽  
X Ray Diffraction ◽  
Photon Detection ◽  
X Ray ◽  
Threshold Detection ◽  
Interesting Alternative

Protein dynamics contribute to protein function on different time scales. Ultrafast X-ray diffraction snapshots can visualize the location and amplitude of atom displacements after perturbation. Since amplitudes of ultrafast motions are small, high-quality X-ray diffraction data is necessary for detection. Diffraction from bovine trypsin crystals using single femtosecond X-ray pulses was recorded at FemtoMAX, which is a versatile beamline of the MAX IV synchrotron. The time-over-threshold detection made it possible that single photons are distinguishable even under short-pulse low-repetition-rate conditions. The diffraction data quality from FemtoMAX beamline enables atomic resolution investigation of protein structures. This evaluation is based on the shape of the Wilson plot, cumulative intensity distribution compared with theoretical distribution, I/σ, R merge/R meas and CC1/2 statistics versus resolution. The FemtoMAX beamline provides an interesting alternative to X-ray free-electron lasers when studying reversible processes in protein crystals.

X-ray film as a two-dimensional detector for X-ray diffraction analysis

2003 ◽  
Vol 18 (2) ◽  
pp. 91-98 ◽  
Author(s):  
T. N. Blanton
Keyword(s):  
Diffraction Analysis ◽  
Spatial Resolution ◽  
Diffraction Data ◽  
High Spatial Resolution ◽  
Silver Halide ◽  
X Rays ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Film Composition ◽  
X Ray

Silver halide based photographic imaging elements have been utilized as detectors for X-rays for over 100 years. These elements comprised of gelatin dispersed silver halide coated on one or both sides of a support, have been utilized in diffraction experiments since the discovery of X-ray diffraction by Laue and co-workers. X-ray film has high spatial resolution and can be adapted to flat or curved two-dimensional detection geometries. This paper describes the use of X-ray film as a two-dimensional detector for X-ray diffraction analysis, and discusses X-ray film composition, exposure, and processing, along with considerations for analyzing X-ray diffraction data collected using X-ray film.

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