An alternative method for data analysis in serial femtosecond crystallography

2014 ◽  
Vol 70 (6) ◽  
pp. 670-676 ◽  
Author(s):  
Tao Zhang ◽  
Yang Li ◽  
Lijie Wu
Keyword(s):  
Data Analysis ◽  
Intensity Distribution ◽  
Diffraction Data ◽  
Free Electron Laser ◽  
Atomic Resolution ◽  
Diffraction Intensity ◽  
Simulation Data ◽  
X Ray ◽  
Structure Factors ◽  
Serial Femtosecond Crystallography

Serial femtosecond crystallography (SFX) [Chapmanet al.(2011),Nature,470, 73–77], based on the X-ray free-electron laser, is a new and powerful tool for structure analysis at atomic resolution. This study proposes an extrapolation method for diffraction data analysis on the basis of diffraction intensity distribution in reciprocal space. Results show that this new method can restore SFX simulation data to structure factors that are more consistent with the structures used in simulation.

scholarly journals EM-detwin: A Program for Resolving Indexing Ambiguity in Serial Crystallography Using the Expectation-Maximization Algorithm

Crystals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 588
Author(s):  
Yingchen Shi ◽  
Haiguang Liu
Keyword(s):  
Data Analysis ◽  
Diffraction Data ◽  
Expectation Maximization ◽  
Expectation Maximization Algorithm ◽  
Atomic Resolution ◽  
Group Symmetry ◽  
Bravais Lattice ◽  
Free Electron Lasers ◽  
X Ray ◽  
Serial Crystallography

Serial crystallography (SX), first used as an application of X-ray free-electron lasers (XFELs), is becoming a useful method to determine atomic-resolution structures of proteins from micrometer-sized crystals with bright X-ray sources. Because of unknown orientations of crystals in SX, indexing ambiguity issue arises when the symmetry of Bravais lattice is higher than the space group symmetry, making some diffraction signals wrongly merged to the total intensity in twinned orientations. In this research, we developed a program within the CrystFEL framework, the EM-detwin, to resolve this indexing ambiguity problem based on the expectation-maximization algorithm. Testing results on the performance of the EM-detwin have demonstrated its usefulness in correctly indexing diffraction data as a valuable tool for SX data analysis.

New method to measure domain-wall motion contribution to piezoelectricity: the case of PbZr0.65Ti0.35O3 ferroelectric

2020 ◽  
Vol 53 (4) ◽  
pp. 1039-1050
Author(s):  
Semën Gorfman ◽  
Hyeokmin Choe ◽  
Guanjie Zhang ◽  
Nan Zhang ◽  
Hiroko Yokota ◽  
...  
Keyword(s):  
Data Analysis ◽  
Domain Wall ◽  
Electric Field ◽  
Intensity Distribution ◽  
Wall Motion ◽  
Domain Wall Motion ◽  
Lattice Parameters ◽  
New Method ◽  
Diffraction Intensity ◽  
X Ray

A new data analysis routine is introduced to reconstruct the change in lattice parameters in individual ferroelastic domains and the role of domain-wall motion in the piezoelectric effect. Using special electronics for the synchronization of a PILATUS X-ray area detector with a voltage signal generator, the X-ray diffraction intensity distribution was measured around seven split Bragg peaks as a function of external electric field. The new data analysis algorithm allows the calculation of `extrinsic' (related to domain-wall motion) and `intrinsic' (related to the change in lattice parameters) contributions to the electric-field-induced deformation. Compared with previously existing approaches, the new method benefits from the availability of a three-dimensional diffraction intensity distribution, which enables the separation of Bragg peaks diffracted from differently oriented domain sets. The new technique is applied to calculate the extrinsic and intrinsic contributions to the piezoelectricity in a single crystal of the ferroelectric PbZr1−x Ti x O3 (x = 0.35). The root-mean-square value of the piezoelectric coefficient was obtained as 112 pC N−1. The contribution of the domain-wall motion is estimated as 99 pC N−1. The contribution of electric-field-induced changes to the lattice parameters averaged over all the domains is 71 pC N−1. The equivalent value corresponding to the change in lattice parameters in individual domains may reach up to 189 pC N−1.

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.

Time-Resolved Serial Femtosecond Crystallography at the European X-ray Free Electron Laser

2019 ◽  
Author(s):  
Marius Schmidt ◽  
Suraj Pandey ◽  
Adrian Mancuso ◽  
Richard Bean
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Crystallographic Data ◽  
Time Resolved ◽  
X Ray ◽  
Serial Femtosecond Crystallography

Abstract This protocol introduces step by step into the collection of time resolved crystallographic data and their analysis at the European Free Electron Laser.

scholarly journals AUSPEX: a graphical tool for X-ray diffraction data analysis

2017 ◽  
Vol 73 (9) ◽  
pp. 729-737 ◽  
Author(s):  
Andrea Thorn ◽  
James Parkhurst ◽  
Paul Emsley ◽  
Robert A. Nicholls ◽  
Melanie Vollmar ◽  
...  
Keyword(s):  
Data Analysis ◽  
Diffraction Data ◽  
Software Tool ◽  
Data Conversion ◽  
Data Sets ◽  
X Ray Diffraction ◽  
X Ray ◽  
Pixel Detectors ◽  
Graphical Tool ◽  
Data Acquisition And Processing

In this paper,AUSPEX, a new software tool for experimental X-ray data analysis, is presented. Exploring the behaviour of diffraction intensities and the associated estimated uncertainties facilitates the discovery of underlying problems and can help users to improve their data acquisition and processing in order to obtain better structural models. The program enables users to inspect the distribution of observed intensities (or amplitudes) against resolution as well as the associated estimated uncertainties (sigmas). It is demonstrated howAUSPEXcan be used to visually and automatically detect ice-ring artefacts in integrated X-ray diffraction data. Such artefacts can hamper structure determination, but may be difficult to identify from the raw diffraction images produced by modern pixel detectors. The analysis suggests that a significant portion of the data sets deposited in the PDB contain ice-ring artefacts. Furthermore, it is demonstrated how other problems in experimental X-ray data caused, for example, by scaling and data-conversion procedures can be detected byAUSPEX.

D-67 High-Resolution X-ray Diffraction Data Analysis From The Partly Relaxed Semiconductor Structures

2009 ◽  
Vol 24 (2) ◽  
pp. 171-171
Author(s):  
A. Ulyanenkov ◽  
A. Benediktovitch ◽  
I. Feranchuk ◽  
B. He ◽  
H. Ress
Keyword(s):  
Data Analysis ◽  
High Resolution ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray ◽  
Semiconductor Structures

scholarly journals Liquid sample delivery techniques for serial femtosecond crystallography

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130337 ◽  
Author(s):  
Uwe Weierstall
Keyword(s):  
Flow Rate ◽  
Free Electron ◽  
Repetition Rate ◽  
Free Electron Laser ◽  
Room Temperature ◽  
Liquid Flow Rate ◽  
Free Electron Lasers ◽  
Liquid Sample ◽  
X Ray ◽  
Serial Femtosecond Crystallography

X-ray free-electron lasers overcome the problem of radiation damage in protein crystallography and allow structure determination from micro- and nanocrystals at room temperature. To ensure that consecutive X-ray pulses do not probe previously exposed crystals, the sample needs to be replaced with the X-ray repetition rate, which ranges from 120 Hz at warm linac-based free-electron lasers to 1 MHz at superconducting linacs. Liquid injectors are therefore an essential part of a serial femtosecond crystallography experiment at an X-ray free-electron laser. Here, we compare different techniques of injecting microcrystals in solution into the pulsed X-ray beam in vacuum. Sample waste due to mismatch of the liquid flow rate to the X-ray repetition rate can be addressed through various techniques.

scholarly journals Determination of crystallographic intensities from sparse data

IUCrJ ◽  
2015 ◽  
Vol 2 (1) ◽  
pp. 29-34 ◽  
Author(s):  
Kartik Ayyer ◽  
Hugh T. Philipp ◽  
Mark W. Tate ◽  
Jennifer L. Wierman ◽  
Veit Elser ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Crystal Size ◽  
Three Dimensional ◽  
Sparse Data ◽  
Data Sets ◽  
X Rays ◽  
Diffraction Intensity ◽  
X Ray ◽  
Proof Of Principle

X-ray serial microcrystallography involves the collection and merging of frames of diffraction data from randomly oriented protein microcrystals. The number of diffracted X-rays in each frame is limited by radiation damage, and this number decreases with crystal size. The data in the frame are said to be sparse if too few X-rays are collected to determine the orientation of the microcrystal. It is commonly assumed that sparse crystal diffraction frames cannot be merged, thereby setting a lower limit to the size of microcrystals that may be merged with a given source fluence. TheEMCalgorithm [Loh & Elser (2009),Phys. Rev. E,80, 026705] has previously been applied to reconstruct structures from sparse noncrystalline data of objects with unknown orientations [Philippet al.(2012),Opt. Express,20, 13129–13137; Ayyeret al.(2014),Opt. Express,22, 2403–2413]. Here, it is shown that sparse data which cannot be oriented on a per-frame basis can be used effectively as crystallographic data. As a proof-of-principle, reconstruction of the three-dimensional diffraction intensity using sparse data frames from a 1.35 kDa molecule crystal is demonstrated. The results suggest that serial microcrystallography is, in principle, not limited by the fluence of the X-ray source, and collection of complete data sets should be feasible at, for instance, storage-ring X-ray sources.

Deconvolution–convolution treatment on powder diffraction data collected with CuKα X-ray and NiKβ filter

2018 ◽  
Vol 33 (2) ◽  
pp. 80-87 ◽  
Author(s):  
Takashi Ida ◽  
Shoki Ono ◽  
Daiki Hattan ◽  
Takehiro Yoshida ◽  
Yoshinobu Takatsu ◽  
...  
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Background Intensity ◽  
Intensity Data ◽  
Powder Diffraction Data ◽  
Diffraction Intensity ◽  
Powder Specimen ◽  
One Dimensional ◽  
X Ray ◽  
Strip Detector

A method to remove small CuKβ peaks and step structures caused by NiK-edge absorption as well as CuKα2 sub-peaks from powder diffraction intensity data measured with Cu-target X-ray source and Ni-foil filter is proposed. The method is based on deconvolution–convolution treatment applying scale transform of abscissa, Fourier transform, and a realistic spectroscopic model for the source X-ray. The validity of the method has been tested by analysis of the powder diffraction data of a standard LaB6 powder (NIST SRM660a) sample, collected with the combination of CuKα X-ray source, Ni-foil Kβ filter, flat powder specimen and one-dimensional Si strip detector. The diffraction intensity data treated with the method have certainly shown background intensity profile without CuKβ peaks and NiK-edge step structures.

scholarly journals OnDA: online data analysis and feedback for serial X-ray imaging

2016 ◽  
Vol 49 (3) ◽  
pp. 1073-1080 ◽  
Author(s):  
Valerio Mariani ◽  
Andrew Morgan ◽  
Chun Hong Yoon ◽  
Thomas J. Lane ◽  
Thomas A. White ◽  
...  
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Free Electron ◽  
Free Electron Laser ◽  
Online Data ◽  
Essential Information ◽  
X Ray ◽  
X Ray Imaging ◽  
The Face ◽  
Online Feedback

This article describes a free and open-source data analysis utility designed for fast online feedback during serial X-ray diffraction and scattering experiments:OnDA(online data analysis). Three complete real-time monitors for common types of serial X-ray imaging experiments are presented. These monitors are capable of providing the essential information required for quick decision making in the face of extreme rates of data collection. In addition, a set of modules, functions and algorithms that allow developers to modify the provided monitors or develop new ones are provided. The emphasis here is on simple, modular and scalable code that is based on open-source libraries and protocols.OnDAmonitors have already proven to be invaluable tools in several experiments, especially for scoring and monitoring of diffraction data during serial crystallography experiments at both free-electron laser and synchrotron facilities. It is felt that in the future the kind of fast feedback thatOnDAmonitors provide will help researchers to deal with the expected very high throughput data flow at next-generation facilities such as the European X-ray free-electron laser.

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