scholarly journals On the release ofcppxfelfor processing X-ray free-electron laser images

2016 ◽  
Vol 49 (3) ◽  
pp. 1065-1072 ◽  
Author(s):  
Helen Mary Ginn ◽  
Gwyndaf Evans ◽  
Nicholas K. Sauter ◽  
David Ian Stuart
Keyword(s):  
Data Analysis ◽  
Free Electron ◽  
Free Electron Laser ◽  
Software Package ◽  
Light Sources ◽  
Data Sets ◽  
Delivery Methods ◽  
Data Set ◽  
X Ray ◽  
Software Packages

As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Herecppxfel, a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set.Cppxfelis released with the hope that the unique and useful elements of this package can be repurposed for existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.

scholarly journals Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser

2019 ◽  
Vol 75 (8) ◽  
pp. 547-551 ◽  
Author(s):  
Robert J. Trachman ◽  
Jason R. Stagno ◽  
Chelsie Conrad ◽  
Christopher P. Jones ◽  
Pontus Fischer ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Free Electron ◽  
Free Electron Laser ◽  
Structural Model ◽  
Data Sets ◽  
Data Set ◽  
X Ray ◽  
Turn On

Turn-on aptamers are in vitro-selected RNAs that bind to conditionally fluorescent small molecules and enhance their fluorescence. Upon binding TO1-biotin, the iMango-III aptamer achieves the largest fluorescence enhancement reported for turn-on aptamers (over 5000-fold). This aptamer was generated by structure-guided engineering and functional reselection of the parental aptamer Mango-III. Structures of both Mango-III and iMango-III have previously been determined by conventional cryocrystallography using synchrotron X-radiation. Using an X-ray free-electron laser (XFEL), the room-temperature iMango-III–TO1-biotin co-crystal structure has now been determined at 3.0 Å resolution. This structural model, which was refined against a data set of ∼1300 diffraction images (each from a single crystal), is largely consistent with the structures determined from single-crystal data sets collected at 100 K. This constitutes a technical benchmark on the way to XFEL pump–probe experiments on fluorescent RNA–small molecule complexes.

scholarly journals Resolving indexing ambiguities in X-ray free-electron laser diffraction patterns

2019 ◽  
Vol 75 (2) ◽  
pp. 234-241
Author(s):  
Monarin Uervirojnangkoorn ◽  
Artem Y. Lyubimov ◽  
Qiangjun Zhou ◽  
William I. Weis ◽  
Axel T. Brunger
Keyword(s):  
Diffraction Data ◽  
Free Electron ◽  
Free Electron Laser ◽  
Bravais Lattice ◽  
Data Sets ◽  
Diffraction Image ◽  
Acta Cryst ◽  
Data Set ◽  
X Ray ◽  
Automated Method

Processing X-ray free-electron laser (XFEL) diffraction images poses challenges, as an XFEL pulse is powerful enough to destroy or damage the diffracting volume and thereby yields only one diffraction image per volume. Moreover, the crystal is stationary during the femtosecond pulse, so reflections are generally only partially recorded. Therefore, each XFEL diffraction image must be scaled individually and, ideally, corrected for partiality prior to merging. An additional complication may arise owing to indexing ambiguities when the symmetry of the Bravais lattice is higher than that of the space group, or when the unit-cell dimensions are similar to each other. Here, an automated method is presented that diagnoses these indexing ambiguities based on the Brehm–Diederichs algorithm [Brehm & Diederichs (2014), Acta Cryst. D70, 101–109] and produces a consistent indexing choice for the large majority of diffraction images. This method was applied to an XFEL diffraction data set measured from crystals of the neuronal SNARE–complexin-1–synaptotagmin-1 complex. After correcting the indexing ambiguities, substantial improvements were observed in the merging statistics and the atomic model refinement R values. This method should be a useful addition to the arsenal of tools for the processing of XFEL diffraction data sets.

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.

scholarly journals Femtosecond free-electron laser x-ray diffraction data sets for algorithm development

2012 ◽  
Vol 20 (4) ◽  
pp. 4149 ◽  
Author(s):  
Stephan Kassemeyer ◽  
Jan Steinbrener ◽  
Lukas Lomb ◽  
Elisabeth Hartmann ◽  
Andrew Aquila ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Free Electron ◽  
Free Electron Laser ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Algorithm Development ◽  
X Ray

scholarly journals Transverse gradient in Apple-type undulators

2017 ◽  
Vol 24 (3) ◽  
pp. 600-608 ◽  
Author(s):  
M. Calvi ◽  
C. Camenzuli ◽  
E. Prat ◽  
Th. Schmidt
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Polarized Light ◽  
Light Sources ◽  
X Ray ◽  
Flexible Devices ◽  
Delta Type ◽  
Transverse Gradient ◽  
New Generation ◽  
Operational Modes

Apple-type undulators are globally recognized as the most flexible devices for the production of variable polarized light in the soft X-ray regime, both at synchrotron and free-electron laser facilities. Recently, the implementation of transverse gradient undulators has been proposed to enhance the performance of new generation light sources. In this paper it is demonstrated that Apple undulators do not only generate linear and elliptical polarized light but also variable transverse gradient under certain conditions. A general theoretical framework is introduced to evaluate the K-value and its transverse gradient for an Apple undulator, and formulas for all regular operational modes and different Apple types (including the most recent Delta type and Apple X) are calculated and critically discussed.

scholarly journals Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser

2019 ◽  
Vol 75 (7) ◽  
pp. 496-500
Author(s):  
Christopher Jones ◽  
Brandon Tran ◽  
Chelsie Conrad ◽  
Jason Stagno ◽  
Robert Trachman ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Small Molecules ◽  
Free Electron ◽  
Free Electron Laser ◽  
Room Temperature ◽  
Temperature Structure ◽  
Data Set ◽  
Time Resolved ◽  
Regulate Gene Expression ◽  
X Ray

Riboswitches are conformationally dynamic RNAs that regulate gene expression by binding specific small molecules. ZTP riboswitches bind the purine-biosynthetic intermediate 5-aminoimidazole-4-carboxamide riboside 5′-monophosphate (ZMP) and its triphosphorylated form (ZTP). Ligand binding to this riboswitch ultimately upregulates genes involved in folate and purine metabolism. Using an X-ray free-electron laser (XFEL), the room-temperature structure of the Fusobacterium ulcerans ZTP riboswitch bound to ZMP has now been determined at 4.1 Å resolution. This model, which was refined against a data set from ∼750 diffraction images (each from a single crystal), was found to be consistent with that previously obtained from data collected at 100 K using conventional synchrotron X-radiation. These experiments demonstrate the feasibility of time-resolved XFEL experiments to understand how the ZTP riboswitch accommodates cognate ligand binding.

scholarly journals Data acquisition system for X-ray free-electron laser experiments at SACLA

2015 ◽  
Vol 22 (3) ◽  
pp. 571-576 ◽  
Author(s):  
Yasumasa Joti ◽  
Takashi Kameshima ◽  
Mitsuhiro Yamaga ◽  
Takashi Sugimoto ◽  
Kensuke Okada ◽  
...  
Keyword(s):  
Data Analysis ◽  
Data Acquisition ◽  
Data Storage ◽  
Free Electron ◽  
Free Electron Laser ◽  
Data Acquisition System ◽  
Acquisition System ◽  
X Ray ◽  
High Data ◽  
Laser Experiments

A data acquisition system for X-ray free-electron laser experiments at SACLA has been developed. The system has been designed for reliable shot-to-shot data storage with a high data stream greater than 4 Gbps and massive data analysis. Configuration of the system and examples of prompt data analysis during experiments are presented. Upgrade plans for the system to extend flexibility are described.

Data Analysis Environment for X-ray Free-Electron Laser Experiments at SACLA

2017 ◽  
Vol 30 (1) ◽  
pp. 16-21 ◽  
Author(s):  
Yasumasa Joti ◽  
Kyo Nakajima ◽  
Takashi Kameshima ◽  
Mitsuhiro Yamaga ◽  
Toshinori Abe ◽  
...  
Keyword(s):  
Data Analysis ◽  
Free Electron ◽  
Free Electron Laser ◽  
X Ray ◽  
Laser Experiments ◽  
Analysis Environment
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