scholarly journals The slip-and-slide algorithm: a refinement protocol for detector geometry

2017 ◽  
Vol 24 (6) ◽  
pp. 1152-1162 ◽  
Author(s):  
Helen Mary Ginn ◽  
David Ian Stuart
Keyword(s):  
Detector Distance ◽  
Detector Geometry ◽  
Linac Coherent Light Source ◽  
Anomalous Signal ◽  
Diffraction Patterns ◽  
A Minor ◽  
Unit Cell Dimensions ◽  
Geometry Method ◽  
Segmented Detectors ◽  
Correlated Parameters

Geometry correction is traditionally plagued by mis-fitting of correlated parameters, leading to local minima which prevent further improvements. Segmented detectors pose an enhanced risk of mis-fitting: even a minor confusion of detector distance and panel separation can prevent improvement in data quality. The slip-and-slide algorithm breaks down effects of the correlated parameters and their associated target functions in a fundamental shift in the approach to the problem. Parameters are never refined against the components of the data to which they are insensitive, providing a dramatic boost in the exploitation of information from a very small number of diffraction patterns. This algorithm can be applied to exploit the adherence of the spot-finding results prior to indexing to a given lattice using unit-cell dimensions as a restraint. Alternatively, it can be applied to the predicted spot locations and the observed reflection positions after indexing from a smaller number of images. Thus, the indexing rate can be boosted by 5.8% using geometry refinement from only 125 indexed patterns or 500 unindexed patterns. In one example of cypovirus type 17 polyhedrin diffraction at the Linac Coherent Light Source, this geometry refinement reveals a detector tilt of 0.3° (resulting in a maximal Z-axis error of ∼0.5 mm from an average detector distance of ∼90 mm) whilst treating all panels independently. Re-indexing and integrating with updated detector geometry reduces systematic errors providing a boost in anomalous signal of sulfur atoms by 20%. Due to the refinement of decoupled parameters, this geometry method also reaches convergence.

scholarly journals Crystal orientation and detector distance effects on resolving pseudosymmetry by electron backscatter diffraction

2021 ◽  
Vol 54 (2) ◽  
pp. 513-522
Author(s):  
Edward L. Pang ◽  
Christopher A. Schuh
Keyword(s):  
Crystal Orientation ◽  
Electron Backscatter Diffraction ◽  
Detector Distance ◽  
Recent Emergence ◽  
Distance Effects ◽  
Electron Backscatter ◽  
Sample Position ◽  
Position And Orientation ◽  
Diffraction Patterns ◽  
Backscatter Diffraction

Accurately indexing pseudosymmetric materials has long proven challenging for electron backscatter diffraction. The recent emergence of intensity-based indexing approaches promises an enhanced ability to resolve pseudosymmetry compared with traditional Hough-based indexing approaches. However, little work has been done to understand the effects of sample position and orientation on the ability to resolve pseudosymmetry, especially for intensity-based indexing approaches. Thus, in this work the effects of crystal orientation and detector distance in a model tetragonal ZrO2 (c/a = 1.0185) material are quantitatively investigated. The orientations that are easiest and most difficult to correctly index are identified, the effect of detector distance on indexing confidence is characterized, and these trends are analyzed on the basis of the appearance of specific zone axes in the diffraction patterns. The findings also point to the clear benefit of shorter detector distances for resolving pseudosymmetry using intensity-based indexing approaches.

Optimal Calibration Curves for Guinier-Type Focusing Cameras

1977 ◽  
Vol 21 ◽  
pp. 289-303
Author(s):  
Allan Brown
Keyword(s):  
Unit Cell ◽  
Routine Measurement ◽  
Calibration Curves ◽  
Cell Dimensions ◽  
Diffraction Patterns ◽  
To Come ◽  
Unit Cell Dimensions ◽  
Optimal Calibration

The inclusion of an internal calibrant in specimens prepared for Guinier-type focusing cameras is a well-established practice. The true reasons for performing calibration are, however, not always clearly understood. Accordingly, procedures adopted on the basis of this calibration for converting distances measured on the film into reliable values of θ vary in detail from one laboratory to another. The possibility that calibration curves can exhibit different degrees of reliability, depending upon camera alignment, is even less generally appreciated. The following account records efforts made over the years to come to terms with these problems in order to obtain unit cell dimensions at the 0.01 % level of precision from the routine measurement of Guinier diffraction patterns.

scholarly journals Structures of pseudo-decagonal approximants in Al−Co−Ni

2012 ◽  
Vol 370 (1969) ◽  
pp. 2949-2959 ◽  
Author(s):  
Sven Hovmöller ◽  
Linus Hovmöller Zou ◽  
Xiaodong Zou ◽  
Benjamin Grushko
Keyword(s):  
High Resolution Electron Microscopy ◽  
Limited Information ◽  
X Ray ◽  
X Ray Crystallography ◽  
Resolution Electron ◽  
Cell Dimensions ◽  
Diffraction Patterns ◽  
Quasi Crystals ◽  
Unit Cell Dimensions ◽  
Microscopy Images

Quasi-crystals shocked the crystallographic world when they were reported in 1984. We now know that they are not a rare exception, and can be found in many alloy systems. One of the richer systems for quasi-crystals and their approximants is Al−Co−Ni. A large series of pseudo-decagonal (PD) approximants have been found. Only two of them, PD4 and PD8, have been solved by X-ray crystallography. We report here the structures of PD1, PD2, PD3 and PD5, solved from the limited information that is provided by electron diffraction patterns, unit cell dimensions and high-resolution electron microscopy images.

scholarly journals The crystal structures of two polyamides (‘nylons’)

1947 ◽  
Vol 189 (1016) ◽  
pp. 39-68 ◽  
Keyword(s):  
Crystal Structures ◽  
Unit Cell ◽  
Chain Molecule ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Dimensions ◽  
C Fibre ◽  
Diffraction Patterns ◽  
Unit Cell Dimensions ◽  
Crystalline Forms

Detailed interpretations of the X -ray diffraction patterns of fibres and sheets of 66 and 6.10 polyamides (polyhexam ethylene adipamide and sebacamide respectively) are proposed. The crystal structures of the two substances are completely analogous. Fibres of these two polyam ides usually contain two different crystalline forms, α and β, which are different packings of geometrically similar molecules; most fibres consist chiefly of the α form. In the case of the 66 polymer, fibres have been obtained in which there is no detectable proportion of the β form. Unit cell dimensions and the indices of reflexions for the α form were determined by trial, using normal fibre photographs, and were checked by using doubly oriented sheets set at different angles to the X -ray beam. The unit cell of the a form is triclinic, with a — 4·9 A, b = 5·4 A, c (fibre axis) = 17·2A, α = 48 1/2º, β = 77º, γ = 63 1/2º for the 66 polymer; a = 4·95A, b = 5·4A, c (fibre axes) = 22·4A, α = 49º, β = 76 1/2º, γ = 63 1/2º for the 6.10 polymer. One chain molecule passes through the cell in both cases. Atomic coordinates in occrystals were determined by interpretation of the relative intensities of the reflexions. The chains are planar or very nearly so; the oxygen atoms appear to lie a little off the plane of the chain. The molecules are linked by hydrogen bonds between C = 0 and NH groups, to form sheets. A simple packing of these sheets of molecules gives the α arrangement.

In-house characterization of protein powder

2010 ◽  
Vol 43 (4) ◽  
pp. 876-882 ◽  
Author(s):  
Christian Grundahl Hartmann ◽  
Ole Faurskov Nielsen ◽  
Kenny Ståhl ◽  
Pernille Harris
Keyword(s):  
Powder Diffraction ◽  
Data Bank ◽  
Lorentz Factor ◽  
Cell Parameters ◽  
Geometric Factors ◽  
Diffraction Patterns ◽  
A Minor ◽  
Coordinate Data ◽  
Good Agreement

X-ray powder diffraction patterns of lysozyme and insulin were recorded on a standard in-house powder diffractometer. The experimental powder diffraction patterns were compared with patterns calculated from Protein Data Bank coordinate data. Good agreement was obtained by including straightforward corrections for background, unit-cell parameters, disordered bulk solvent and geometric factors. In particular the solvent correction was found crucial for a good agreement. A revised Lorentz factor was derived, which gave a minor, but significant, improvement to the fit in the low-angle region. An attempt to include calculated H-atom positions did not improve the overall fit and was abandoned. The method devised was shown to be a quick and convenient tool for distinguishing precipitates and polymorphs of proteins.

An analysis of preferred orientation in YBa2Cu3O7–x superconducting films deposited by CVD on single-crystal and polycrystalline substrates

1994 ◽  
Vol 9 (4) ◽  
pp. 250-259 ◽  
Author(s):  
E. A. Judson ◽  
D. N. Hill ◽  
R. A. Young ◽  
J. R. Cagle ◽  
W. J. Lackey ◽  
...  
Keyword(s):  
Single Crystal ◽  
Chemical Vapor ◽  
Preferred Orientation ◽  
Superconducting Properties ◽  
High Temperature Anneal ◽  
Pole Figures ◽  
Before And After ◽  
Diffraction Patterns ◽  
A Minor ◽  
Orientation Phenomenon

YBa2Cu3O7–x films were deposited by chemical vapor deposition (CVD) onto single-crystal MgO, single-crystal Al2O3, and polycrystalline Al2O3 substrates, characterized before and after annealing, and tested for their superconducting properties. The preferred orientation in the films was analyzed (i) with pole figures and (ii) by comparison of experimental x-ray powder diffraction patterns with those calculated for the material using the March–Dollase function to model the degree of preferred orientation. Preferred orientation was significant in as-deposited films, with March coefficients ranging from 0.1–0.5 (random orientation would have a coefficient of 1.0). The (006) pole figures of the films on single crystal substrates exhibited uniquely symmetric patterns. On single-crystal MgO before annealing, a minor secondary orientation of (006) poles in the film was observed in a pattern consistent with the symmetry of major crystallographic directions of MgO. On single-crystal Al2O3 after annealing, a “dual orientation” phenomenon was observed. The high-temperature anneal destroyed the orientation and superconducting properties of the CVD films deposited at high temperatures.

scholarly journals Research at the NSF STC for Biology with X-ray lasers

2014 ◽  
Vol 70 (a1) ◽  
pp. C296-C296
Author(s):  
John Spence
Keyword(s):  
Radiation Damage ◽  
Bragg Diffraction ◽  
Cubic Phase ◽  
Short Pulses ◽  
X Ray ◽  
Fast Solution ◽  
Linac Coherent Light Source ◽  
New Ideas ◽  
Diffraction Patterns ◽  
Dynamic Structures

"The NSF BioXFEL Science and Technology Center (STC) is a new consortium of six research campuses devoted to the application of x-ray free-electron lasers (XFELs) to structural biology. Over the last four years a variety of approaches have been made to the observation of protein structure and dynamics for various classes of proteins. The Linac Coherent Light source at SLAC, the first hard-Xray EXFEL, provides intense coherent hard X-ray pulses at 120 Hz which vaporize protein when focussed to a sub-micron beam. Atomic-resolution Bragg diffraction patterns are nevertheless obtained using 50 fs pulses prior to the onset of significant damage, in this ""diffract-then-destroy"" mode, which outruns radiation damage. This use of short pulses instead of freezing samples to reduce radiation damage therefore opens the way to the study of protein dynamics at room temperature in a native environment. I'll review the work of several groups using a range of approaches to different types of sample, including the following: 1. Differences between the frozen sychrotron structure of GPCR proteins and the RT XFEL structure [1]. 2. Pump-probe dynamic structures in Photosynthesis [2]. 3. XFEL study of 2D protein crystals [3]. 4. Prospects for improved resolution in XFEL imaging from single particles such as viruses, where patterns can be obtained from a single virus. 5. New ideas - the Lipid Cubic Phase injector (which allows protein nanocrystals to be studied also at sychrotrons) [4], prospects for fast Laue diffraction using coherent attosecond X-ray lasers, ab-initio phasing [5], the use of angular correlation functions for analysis of fast solution scattering, and two-color opportunites for serial femtosecond crystallography (SFX). See [6] for a recent review of the field. 1. W.Liu et al Science 342, 1521 (2013) 2. A.Aquila et al Optics Express 20, 2706 (2012) 3. M.Frank et al IUCrJ (2014) In press. 4. U.Weierstall et al Nature Comms. (2014) In press. 5. J. Spence et al Optics Express 19, 2866 (2011). 6. J. Spence et al Rep. Prog. Phys. 75, 102601 (2012)."

Unit cell dimensions of the hydrated aluminium phosphate–sulphate minerals sanjuanite, kribergite, and hotsonite

1989 ◽  
Vol 53 (371) ◽  
pp. 385-386 ◽  
Author(s):  
H. De Bruiyn ◽  
G. J. Beukes ◽  
W. A. Van Der Westhuizen ◽  
E. A. W. Tordiffe
Keyword(s):  
Unit Cell ◽  
X Ray Diffraction ◽  
Aluminium Phosphate ◽  
Powder Diffraction File ◽  
Cell Parameters ◽  
Cell Dimensions ◽  
Unit Cells ◽  
Diffraction Patterns ◽  
Unit Cell Dimensions ◽  
Hydrated Aluminium

AT the time when the hydrated aluminium phosphate-sulphate hotsonite (Beukes et al., 1984a) and its equally rare relative zaherite (Beukes et al., 1984b; De Bruiyn et al., 1985) were discovered near Pofadder, South Africa, very little was known about the unit cells of the other two hydrated aluminium phosphate-sulphate minerals sanjuanite and kribergite, originally described by De Abeledo et al. (1968) from Argentina and Sweden, respectively. Although the Powder Diffraction file (PDF) contains the X-ray diffraction patterns for sanjuanite and kribergite (PDF 20-47 and 20-48 respectively), they had not been indexed nor have their unit cell parameters been calculated thus far.

scholarly journals Femtosecond X-ray diffraction from two-dimensional protein crystals

IUCrJ ◽  
2014 ◽  
Vol 1 (2) ◽  
pp. 95-100 ◽  
Author(s):  
Matthias Frank ◽  
David B. Carlson ◽  
Mark S. Hunter ◽  
Garth J. Williams ◽  
Marc Messerschmidt ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Bragg Diffraction ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Linac Coherent Light Source ◽  
Diffraction Patterns ◽  
Better Than

X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.

Determination of lattice-transform density profiles for multilayered three-dimensional microcrystals in electron crystallography

2000 ◽  
Vol 33 (4) ◽  
pp. 1102-1112 ◽  
Author(s):  
Eva Dimmeler ◽  
Oliver Vossen ◽  
Rasmus R. Schröder
Keyword(s):  
Three Dimensional ◽  
Electron Crystallography ◽  
Data Set ◽  
Density Profiles ◽  
New Correlation ◽  
Diffraction Geometry ◽  
Dimensional Shape ◽  
Diffraction Patterns ◽  
Unit Cell Dimensions

Electron crystallography on multilayered three-dimensional microcrystals has been limited in application by the need to define precisely the three-dimensional shape of the diffraction density profiles. A new method is presented here to obtain this profile from experimental spot positions which are shifted in a characteristic way from the expected Bragg positions. While the Bragg positions are defined by the diffraction geometry, the characteristic shift additionally depends on the density profile in Fourier space. In general, these two effects are intermingled. A new correlation approach is presented which uses characteristic shift patterns to separate these effects. This technique also allows the determination of all three crystallographic unit-cell dimensions from a single tilted electron diffraction pattern. It was tested on simulated diffraction patterns and applied to experimental data of frozen hydrated crystals of the protein catalase. Since multilayered catalase crystals with different numbers of crystallographic layers were studied, an inhomogeneous data set had to be evaluated. Processing of such data is now possible using the new correlation approach.

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