Olof Svensson

Fast microtomography using high energy synchrotron radiation

At the High Energy Beamline ID15A at the European Synchrotron Radiation Facility we have developed a fast three-dimensional x-ray microtomography system, which acquires a complete dataset in typically less than 10s. This unprecedented speed is achieved by combining a high efficiency phosphor screen, a reflecting microscope objective and a fast charge coupled device detector with the very intense high-energy white beam radiation provided by a wiggler source. The achieved spatial resolution is 2μm. The available x-ray energy spectrum spans from 20to250keV and can therefore be used for low and high Z materials. The spectrum can be modified by inserting different filters into the x-ray beam in order to optimize the signal-to-noise ratio and to avoid beam-hardening artifacts. Different phosphors with different energy sensitivity can be used. The very high speed allows in situ studies of systems evolving on the time scale of a few seconds or minutes. Three examples are given on sintering of metallic powders, so...

EDNA: a framework for plugin-based applications applied to X-ray experiment online data analysis.

EDNA is a framework for developing plugin-based applications especially for online data analysis in the X-ray experiments field. This article describes the features provided by the EDNA framework to ease the development of extensible scientific applications. This framework includes a plugins class hierarchy, configuration and application facilities, a mechanism to generate data classes and a testing framework. These utilities allow rapid development and integration in which robustness and quality play a fundamental role. A first prototype, designed for macromolecular crystallography experiments and tested at several synchrotrons, is presented.

Data Analysis WorkbeNch (DAWN)

DAWN is a generic data analysis software platform that has been developed for use at synchrotron beamlines for data visualization and analysis. Its generic design makes it suitable for use in a range of scientific and engineering applications.

Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection

Crystals of biological macromolecules often exhibit considerable inter-crystal and intra-crystal variation in diffraction quality. This requires the evaluation of many samples prior to data collection, a practice that is already widespread in macromolecular crystallography. As structural biologists move towards tackling ever more ambitious projects, new automated methods of sample evaluation will become crucial to the success of many projects, as will the availability of synchrotron-based facilities optimized for high-throughput evaluation of the diffraction characteristics of samples. Here, two examples of the types of advanced sample evaluation that will be required are presented: searching within a sample-containing loop for microcrystals using an X-ray beam of 5 microm diameter and selecting the most ordered regions of relatively large crystals using X-ray beams of 5-50 microm in diameter. A graphical user interface developed to assist with these screening methods is also presented. For the case in which the diffraction quality of a relatively large crystal is probed using a microbeam, the usefulness and implications of mapping diffraction-quality heterogeneity (diffraction cartography) are discussed. The implementation of these techniques in the context of planned upgrades to the ESRFs structural biology beamlines is also presented.

ISPyB: an information management system for synchrotron macromolecular crystallography

MOTIVATION Individual research groups now analyze thousands of samples per year at synchrotron macromolecular crystallography (MX) resources. The efficient management of experimental data is thus essential if the best possible experiments are to be performed and the best possible data used in downstream processes in structure determination pipelines. Information System for Protein crystallography Beamlines (ISPyB), a Laboratory Information Management System (LIMS) with an underlying data model allowing for the integration of analyses down-stream of the data collection experiment was developed to facilitate such data management. RESULTS ISPyB is now a multisite, generic LIMS for synchrotron-based MX experiments. Its initial functionality has been enhanced to include improved sample tracking and reporting of experimental protocols, the direct ranking of the diffraction characteristics of individual samples and the archiving of raw data and results from ancillary experiments and post-experiment data processing protocols. This latter feature paves the way for ISPyB to play a central role in future macromolecular structure solution pipelines and validates the application of the approach used in ISPyB to other experimental techniques, such as biological solution Small Angle X-ray Scattering and spectroscopy, which have similar sample tracking and data handling requirements.

High-throughput sample handling and data collection at synchrotrons: embedding the ESRF into the high-throughput gene-to-structure pipeline

An automatic data-collection system has been implemented and installed on seven insertion-device beamlines and a bending-magnet beamline at the ESRF (European Synchrotron Radiation Facility) as part of the SPINE (Structural Proteomics In Europe) development of an automated structure-determination pipeline. The system allows remote interaction with beamline-control systems and automatic sample mounting, alignment, characterization, data collection and processing. Reports of all actions taken are available for inspection via database modules and web services.

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

A system for the automatic reduction of single- and multi-position macromolecular crystallography data is presented.

Fully automatic characterization and data collection from crystals of biological macromolecules

A fully automatic system has been developed that performs X-ray centring and characterization of, and data collection from, large numbers of cryocooled crystals without human intervention.

Meshandcollect: An Automated Multi-Crystal Data-Collection Workflow for Synchrotron Macromolecular Crystallography Beamlines.

The fully automated collection and merging of partial data sets from a series of cryocooled crystals of biological macromolecules contained on the same support is presented, as are the results of test experiments carried out on various systems.

The use of workflows in the design and implementation of complex experiments in macromolecular crystallography.

A powerful and easy-to-use workflow environment has been developed at the ESRF for combining experiment control with online data analysis on synchrotron beamlines. This tool provides the possibility of automating complex experiments without the need for expertise in instrumentation control and programming, but rather by accessing defined beamline services.