O. Svensson - Academia.edu (original) (raw)

Papers by O. Svensson

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

Journal of Applied Crystallography, 2013

The development of automated high-intensity macromolecular crystallography (MX) beamlines at sync... more 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 ...

Research paper thumbnail of Automation of macromolecular crystallography beamlines

Progress in Biophysics and Molecular Biology, 2005

The production of three-dimensional crystallographic structural information of macromolecules can... more The production of three-dimensional crystallographic structural information of macromolecules can now be thought of as a pipeline which is being streamlined at every stage from protein cloning, expression and purification, through crystallisation to data collection and structure solution. Synchrotron X-ray beamlines are a key section of this pipeline as it is at these that the X-ray diffraction data that ultimately leads to the elucidation of macromolecular structures are collected. The burgeoning number of macromolecular crystallography (MX) beamlines available worldwide may be enhanced significantly with the automation of both their operation and of the experiments carried out on them. This paper reviews the current situation and provides a glimpse of how a MX beamline may look in the not too distant future.

Research paper thumbnail of <title>Automatic alignment of a synchrotron radiation source beamline using intelligent systems</title>

Applications and Science of Neural Networks, Fuzzy Systems, and Evolutionary Computation, 1998

ABSTRACT Synchrotron Radiation (SR) sources in general, and the new third generation SR sources i... more ABSTRACT Synchrotron Radiation (SR) sources in general, and the new third generation SR sources in particular, deliver very intense x-ray beams with very low divergence. However, due to small shifts of the sorted electron beam position caused by re-optimization of the closed orbit after shutdowns, the beamlines must be regularly re-aligned in order to deliver optimum performance. Since the beamlines generally contain complicated optical elements, such as x- ray mirrors and monochromators, the alignment procedure is difficult and time-consuming. Automatic beamline alignment has been envisaged in order to more constantly keep optimal performance of the beamline. An Intelligent System approach has been chosen to face the complexity of x-ray beamline alignment. A knowledge-based system has been chosen for the development of the automatic alignment tools. The developed tools have been applied to the multi-wavelength anomalous dispersion (MAD) beamline of the European Synchrotron Radiation (ESRF). The intensity and the spot shape at the sample position, obtained by using a small 2D CCD detector, were optimized by automatically aligning the main optical element, a bent cylindrical mirror that focuses the beam in both horizontal and vertical directions. The developed automatic techniques have been shown to robustly optimize the intensity and the focal spot shape on the ESRF MAD beamline. A series of images of the beam shape showing the optimization will be presented.

Research paper thumbnail of Calibration and correction of spatial distortions in 2D detector systems

Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 1994

Many photon and other radiation 2D detection systems introduce spatial distortions into recorded ... more Many photon and other radiation 2D detection systems introduce spatial distortions into recorded data. As long as these distortions are to some degree repeatable it is possible to use a grid of holes of known positions to illuminate the detector and calibrate the distortion. Knowledge of this distortion can be used to correct subsequent images. Aspects of calibration grid design are discussed with the aim ofachieving optimum results. Cross-correlation with known hole functions is proposed as a method for estimating grid peak centres giving optimum accuracy and efficiency. Strategies to search efficiently complete grids are also presented. Where a physical model of the distortion process is lacking or inadequate, bi-cubic splines are proposed as suitable interpolating functions for defining approximate spatial distortion functions. Bi-cubic splines allow both adequate flexibility to describe arbitrary distortions and, most importantly, to allow efficient calculation for the correction of data. Calibration and correction algorithms have been developed and applied to 2D detector systems. Sample results are presented.

Research paper thumbnail of Time-Resolved X-ray Powder Diffraction Using a Large-Area CCD-Based Detector and Rietveld Refinement: Solid-State Polymerization of S2N2 to (SN)x

Journal of Synchrotron Radiation, 1997

A kinetic study of the solid-state polymerization of disulfur dinitride (S_~N2) to polysulfur nit... more A kinetic study of the solid-state polymerization of disulfur dinitride (S_~N2) to polysulfur nitride [(SN),] has been performed, combining monochromatic high-energy (~\ = 0.3263,~) synchrotron radiation X-ray powder diffraction, a large-area (o = 220 ram) CCD-based X-ray image-intensifier detector and Rietveld refinement. Recently developed techniques for detector calibration and reduction of two-dimensional images to one-dimensional diffraction patterns have been employed for data processing/analysis. Good fits were obtained after Rietveld refinement [Rp = 8.4%, wRp = 9.4%, sin(0.,,,~)/A = 0.585/~ 1] of diffraction patterns of S_~N_~ fiom images with 2 s exposure time. The solid-state polymerization of S2N_~ to (SN), was followed at a maximum rate of two diffraction images per minute. Scale factors and cell parameters for S,N~ and ,J-(SN), as functions o1" time were readily obtained after Rietveld refinement of the diffraction patterns obtained from each individual image throughout the polymerization. The polymerization was preceded by a lattice distortion of S2N~, and at 50% conversion the a axis had decreased by about 1% and the c axis had increased about 1%. The polymerization yielded not only the expected polymer ,~-(SN),, but also a small amount of a compound that could be another phase of (SN),.

Research paper thumbnail of Calibration and Application of an X-ray Image Intensifier/ Charge-Coupled Device Detector for Monochromatic Macromolecular Crystallography

Journal of Synchrotron Radiation, 1997

Charge-coupled device (CCD)-based X-ray detectors allow data to be collected much more quickly (-... more Charge-coupled device (CCD)-based X-ray detectors allow data to be collected much more quickly (-,10 times) than with current on-line imaging-plate systems. At the ESRF, X-ray image intensifier/CCD detector systems have been developed. These have great potential as fast read-out detectors for macromolecular and other forms of crystallography. They are relatively large sensitive X-ray detectors but have two inherent weaknesses: convex detection surfaces leading to spatial distortion and non-uniformity of intensity response, and susceptibility to small changes in magnetic fields. A large improvement has been made to the accuracy obtained by non-uniformity of response calibration and correction, using fluorescence from doped lithium borate glasses. Monochromatic macromolecular crystallography demonstration experiments with external user groups have shown that high-quality results may be obtained under real experimental conditions.

Research paper thumbnail of A Novel Technique for Accurate Intensity Calibration of Area X-ray Detectors at Almost Arbitrary Energy

Journal of Synchrotron Radiation, 1996

A novel intensity uniformity calibration method for area X-ray detectors is described. In diffrac... more A novel intensity uniformity calibration method for area X-ray detectors is described. In diffraction experiments, amorphous lithium glass plates, containing doping elements chosen for their K edges just below the energy of the main beam, replace the crystallographic samples for the calibration measurement. The fluorescent emission excited by the X-ray beam is almost isotropic. It has exactly the same geometry as the diffracted radiation, and can be obtained at the same wavelength by proper selection of the element and excitation energy. A simple 20 scan allows the emission distribution as a function of angle to be characterized with an accuracy of a fraction of a percent. This allows a flat-field correction to a similar accuracy. The quality of crystallographic data collected with an X-ray image intensifier/CCD detector was significantly improved by flat-field correction using an Sr-doped lithium tetraborate glass. This technique can be applied to X-ray energies from 5 to 50 keV; the calibration sample is small, stable and easily handled.

Research paper thumbnail of The point-spread function of X-ray image-intensifiers/CCD-camera and imaging-plate systems in crystallography: assessment and consequences for the dynamic range

Journal of Applied Crystallography, 1994

ABSTRACT The point-spread functions (PSFs) of two X-ray CCD detectors and two imaging-plate (IP) ... more ABSTRACT The point-spread functions (PSFs) of two X-ray CCD detectors and two imaging-plate (IP) scanners were compared using the monochromatic beam of the Materials Science beamline of the ESRF. The CCD detectors were a commercial medical type X-ray image intensifier (XRII) for energies above 20 keV and a tube with a beryllium window especially designed for the 5–50 keV range, optically coupled to a high-resolution cooled charge-coupled-device (CCD) camera. The IP scanners were the Fuji BAS2000 and the Molecular Dynamics PhosphorImager 400E, with plates from Fuji and Kodak. The PSFs were recorded using a 30 × 30 μm pinhole at energies from 8 to 41 keV under normal and highly saturated conditions. Special care was taken in the study of PSF wings. Dynamic range capabilities in the presence of PSF bleeding were also measured using a standard X-ray generator. The Fuji and MD IP scanners give very similar PSFs when used with Fuji plates [ca 130 μm full width at half-maximum (FWHM), 1100 μm at 0.1% of peak maximum]. The Kodak plates showed a broader PSF than the Fuji plates, one which also increases with X-ray energy. The standard XRII/CCD gave the coarsest PSF (ca 4000 μm at 0.1% of peak maximum), whereas the finest PSF was recorded with the beryllium XRII/CCD used in magnified mode (900 μm at 0.1%). The best dynamic range was obtained with the XRII/CCDs; the lowest with the Fuji scanner.

Research paper thumbnail of An X-ray Charge-Density Feasibility Study at 56 keV of Magnesium Formate Dihydrate using a CCD Area Detector

Journal of Applied Crystallography, 1997

A high-resolution structural study of magnesium formate dihydrate was performed using high-energy... more A high-resolution structural study of magnesium formate dihydrate was performed using high-energy synchrotron radiation (0.22 A) and an X-ray image intensifier/CCD (charge-coupled device) detector. The complete data collection was performed in less than 2 h. The data were treated by two different integration programs and the results are compared. The data quality was sufficiently high to produce good-quality electron difference density maps.

Research paper thumbnail of Two-dimensional detector software: From real detector to idealised image or two-theta scan

High Pressure Research, 1996

... TWO-DIMENSIONAL DETECTOR SOFTWARE: FROM REAL DETECTOR TO IDEALISED IMAGE OR TWO-THETA SCAN AP... more ... TWO-DIMENSIONAL DETECTOR SOFTWARE: FROM REAL DETECTOR TO IDEALISED IMAGE OR TWO-THETA SCAN AP HAMMERSLEY*, S. 0. SVENSSON, M. HANFLAND, AN FITCH and D. HAUSERMANN ... 235 Page 2. 236 A. P. HAMMERSLEY et al. ...

Research paper thumbnail of Real-time pursuit of diffusionless phase transition in Ni3Sb using synchrotron radiation

Acta Materialia, 1997

Between 5OO'C and 600°C the intermetailic alloy NiSb undergoes a phase transition between a low-t... more Between 5OO'C and 600°C the intermetailic alloy NiSb undergoes a phase transition between a low-temperature orthorhombic phase and a high-temperature cubic phase. We have studied the progress of the phase transition as a function of time by single-crystal diffraction of monochromatic X-rays provided by a synchrotron in combination with a fast read-out CCD based area detector. On cooling and heating it was possible to follow the transition by registering the progressive splitting, respectively the disappearance of the splitting, of the cubic Bragg reflections. in particular (220) and (422). 0 1997 Acta Metallurgica Inc.

Research paper thumbnail of Protein Crystallography at Ultra-Short Wavelengths: Feasibility Study of Anomalous-Dispersion Experiments at the Xenon K-edge

Journal of Synchrotron Radiation, 1997

A protein crystallography experiment at the xenon K-edge (~. = 0.358 A) has been successfully car... more A protein crystallography experiment at the xenon K-edge (~. = 0.358 A) has been successfully carried out at the materials science beamline (BL2/IDll) of the ESRE The samples used in this methodological study were crystals of porcine pancreatic elastase, a 26 kDa protein of known structure. The diffraction data are of excellent quality. The combination of isomorphous replacement and anomalous dispersion of a single xenon heavy-atom derivative allowed accurate phase determination and the computation of a high-quality electron density map of the protein molecule. This is the first fully documented report on a complete protein crystallography experiment, from data collection up to phase determination and calculation of an electron density map, carried out with data obtained at ultra-short wavelengths. Experimental considerations as well as possible advantages and drawbacks of protein crystallography at very short and ultra-short wavelengths are discussed.

Research paper thumbnail of In Situ , Time-Resolved X-ray Diffraction Study of the Solid-State Polymerization of Disulfur Dinitride to Poly(sulfur nitride)

Inorganic Chemistry, 1997

Products and kinetic and mechanistic aspects of the title reaction were investigated by time-reso... more Products and kinetic and mechanistic aspects of the title reaction were investigated by time-resolved X-ray powder diffraction combined with Rietveld refinement. The polymerization of S(2)N(2) at 40 degrees C was monitored with a time resolution better than one diffraction pattern per minute until completion. The reaction product comprised a mixture of monoclinic beta-(SN)(x)() (90%) and an additional orthorhombic phase, identified as alpha-(SN)(x)() (about 10%). The inversely proportional conversion/formation vs time curves for educt and products indicate that the reaction involves only crystalline phases. The cell parameters of polymerizing S(2)N(2) varied noticeably with progressing conversion, whereas the cell volume remained unchanged up to a monomer conversion of 50%. Refinement of atomic coordinates for S and N indicated retention of the reactant geometry. It is concluded that the polymerization of S(2)N(2) to (SN)(x)() is of nondiffusive nature and involves a martensitic transition.

Research paper thumbnail of ISPyB: an information management system for synchrotron macromolecular crystallography

Bioinformatics, 2011

Individual research groups now analyze thousands of samples per year at synchrotron macromolecula... more 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 synchrotronbased 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.

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

Acta crystallographica. Section D, Biological crystallography, 2006

An automatic data-collection system has been implemented and installed on seven insertion-device ... more 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.

Research paper thumbnail of Automation of the collection and processing of X-ray diffraction data – a generic approach

Acta Crystallographica Section D Biological Crystallography, 2002

Research paper thumbnail of Automation of MX data collection and processing

Acta Crystallographica Section A Foundations of Crystallography, 2005

Research paper thumbnail of Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection

Acta Crystallographica Section D Biological Crystallography, 2010

Author(s) of this paper may load this reprint on their own web site or institutional repository p... more Author(s) of this paper may load this reprint on their own web site or institutional repository provided that this cover page is retained. Republication of this article or its storage in electronic databases other than as specified above is not permitted without prior permission in writing from the IUCr.

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

Journal of Applied Crystallography, 2013

The development of automated high-intensity macromolecular crystallography (MX) beamlines at sync... more 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 ...

Research paper thumbnail of Automation of macromolecular crystallography beamlines

Progress in Biophysics and Molecular Biology, 2005

The production of three-dimensional crystallographic structural information of macromolecules can... more The production of three-dimensional crystallographic structural information of macromolecules can now be thought of as a pipeline which is being streamlined at every stage from protein cloning, expression and purification, through crystallisation to data collection and structure solution. Synchrotron X-ray beamlines are a key section of this pipeline as it is at these that the X-ray diffraction data that ultimately leads to the elucidation of macromolecular structures are collected. The burgeoning number of macromolecular crystallography (MX) beamlines available worldwide may be enhanced significantly with the automation of both their operation and of the experiments carried out on them. This paper reviews the current situation and provides a glimpse of how a MX beamline may look in the not too distant future.

Research paper thumbnail of <title>Automatic alignment of a synchrotron radiation source beamline using intelligent systems</title>

Applications and Science of Neural Networks, Fuzzy Systems, and Evolutionary Computation, 1998

ABSTRACT Synchrotron Radiation (SR) sources in general, and the new third generation SR sources i... more ABSTRACT Synchrotron Radiation (SR) sources in general, and the new third generation SR sources in particular, deliver very intense x-ray beams with very low divergence. However, due to small shifts of the sorted electron beam position caused by re-optimization of the closed orbit after shutdowns, the beamlines must be regularly re-aligned in order to deliver optimum performance. Since the beamlines generally contain complicated optical elements, such as x- ray mirrors and monochromators, the alignment procedure is difficult and time-consuming. Automatic beamline alignment has been envisaged in order to more constantly keep optimal performance of the beamline. An Intelligent System approach has been chosen to face the complexity of x-ray beamline alignment. A knowledge-based system has been chosen for the development of the automatic alignment tools. The developed tools have been applied to the multi-wavelength anomalous dispersion (MAD) beamline of the European Synchrotron Radiation (ESRF). The intensity and the spot shape at the sample position, obtained by using a small 2D CCD detector, were optimized by automatically aligning the main optical element, a bent cylindrical mirror that focuses the beam in both horizontal and vertical directions. The developed automatic techniques have been shown to robustly optimize the intensity and the focal spot shape on the ESRF MAD beamline. A series of images of the beam shape showing the optimization will be presented.

Research paper thumbnail of Calibration and correction of spatial distortions in 2D detector systems

Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 1994

Many photon and other radiation 2D detection systems introduce spatial distortions into recorded ... more Many photon and other radiation 2D detection systems introduce spatial distortions into recorded data. As long as these distortions are to some degree repeatable it is possible to use a grid of holes of known positions to illuminate the detector and calibrate the distortion. Knowledge of this distortion can be used to correct subsequent images. Aspects of calibration grid design are discussed with the aim ofachieving optimum results. Cross-correlation with known hole functions is proposed as a method for estimating grid peak centres giving optimum accuracy and efficiency. Strategies to search efficiently complete grids are also presented. Where a physical model of the distortion process is lacking or inadequate, bi-cubic splines are proposed as suitable interpolating functions for defining approximate spatial distortion functions. Bi-cubic splines allow both adequate flexibility to describe arbitrary distortions and, most importantly, to allow efficient calculation for the correction of data. Calibration and correction algorithms have been developed and applied to 2D detector systems. Sample results are presented.

Research paper thumbnail of Time-Resolved X-ray Powder Diffraction Using a Large-Area CCD-Based Detector and Rietveld Refinement: Solid-State Polymerization of S2N2 to (SN)x

Journal of Synchrotron Radiation, 1997

A kinetic study of the solid-state polymerization of disulfur dinitride (S_~N2) to polysulfur nit... more A kinetic study of the solid-state polymerization of disulfur dinitride (S_~N2) to polysulfur nitride [(SN),] has been performed, combining monochromatic high-energy (~\ = 0.3263,~) synchrotron radiation X-ray powder diffraction, a large-area (o = 220 ram) CCD-based X-ray image-intensifier detector and Rietveld refinement. Recently developed techniques for detector calibration and reduction of two-dimensional images to one-dimensional diffraction patterns have been employed for data processing/analysis. Good fits were obtained after Rietveld refinement [Rp = 8.4%, wRp = 9.4%, sin(0.,,,~)/A = 0.585/~ 1] of diffraction patterns of S_~N_~ fiom images with 2 s exposure time. The solid-state polymerization of S2N_~ to (SN), was followed at a maximum rate of two diffraction images per minute. Scale factors and cell parameters for S,N~ and ,J-(SN), as functions o1" time were readily obtained after Rietveld refinement of the diffraction patterns obtained from each individual image throughout the polymerization. The polymerization was preceded by a lattice distortion of S2N~, and at 50% conversion the a axis had decreased by about 1% and the c axis had increased about 1%. The polymerization yielded not only the expected polymer ,~-(SN),, but also a small amount of a compound that could be another phase of (SN),.

Research paper thumbnail of Calibration and Application of an X-ray Image Intensifier/ Charge-Coupled Device Detector for Monochromatic Macromolecular Crystallography

Journal of Synchrotron Radiation, 1997

Charge-coupled device (CCD)-based X-ray detectors allow data to be collected much more quickly (-... more Charge-coupled device (CCD)-based X-ray detectors allow data to be collected much more quickly (-,10 times) than with current on-line imaging-plate systems. At the ESRF, X-ray image intensifier/CCD detector systems have been developed. These have great potential as fast read-out detectors for macromolecular and other forms of crystallography. They are relatively large sensitive X-ray detectors but have two inherent weaknesses: convex detection surfaces leading to spatial distortion and non-uniformity of intensity response, and susceptibility to small changes in magnetic fields. A large improvement has been made to the accuracy obtained by non-uniformity of response calibration and correction, using fluorescence from doped lithium borate glasses. Monochromatic macromolecular crystallography demonstration experiments with external user groups have shown that high-quality results may be obtained under real experimental conditions.

Research paper thumbnail of A Novel Technique for Accurate Intensity Calibration of Area X-ray Detectors at Almost Arbitrary Energy

Journal of Synchrotron Radiation, 1996

A novel intensity uniformity calibration method for area X-ray detectors is described. In diffrac... more A novel intensity uniformity calibration method for area X-ray detectors is described. In diffraction experiments, amorphous lithium glass plates, containing doping elements chosen for their K edges just below the energy of the main beam, replace the crystallographic samples for the calibration measurement. The fluorescent emission excited by the X-ray beam is almost isotropic. It has exactly the same geometry as the diffracted radiation, and can be obtained at the same wavelength by proper selection of the element and excitation energy. A simple 20 scan allows the emission distribution as a function of angle to be characterized with an accuracy of a fraction of a percent. This allows a flat-field correction to a similar accuracy. The quality of crystallographic data collected with an X-ray image intensifier/CCD detector was significantly improved by flat-field correction using an Sr-doped lithium tetraborate glass. This technique can be applied to X-ray energies from 5 to 50 keV; the calibration sample is small, stable and easily handled.

Research paper thumbnail of The point-spread function of X-ray image-intensifiers/CCD-camera and imaging-plate systems in crystallography: assessment and consequences for the dynamic range

Journal of Applied Crystallography, 1994

ABSTRACT The point-spread functions (PSFs) of two X-ray CCD detectors and two imaging-plate (IP) ... more ABSTRACT The point-spread functions (PSFs) of two X-ray CCD detectors and two imaging-plate (IP) scanners were compared using the monochromatic beam of the Materials Science beamline of the ESRF. The CCD detectors were a commercial medical type X-ray image intensifier (XRII) for energies above 20 keV and a tube with a beryllium window especially designed for the 5–50 keV range, optically coupled to a high-resolution cooled charge-coupled-device (CCD) camera. The IP scanners were the Fuji BAS2000 and the Molecular Dynamics PhosphorImager 400E, with plates from Fuji and Kodak. The PSFs were recorded using a 30 × 30 μm pinhole at energies from 8 to 41 keV under normal and highly saturated conditions. Special care was taken in the study of PSF wings. Dynamic range capabilities in the presence of PSF bleeding were also measured using a standard X-ray generator. The Fuji and MD IP scanners give very similar PSFs when used with Fuji plates [ca 130 μm full width at half-maximum (FWHM), 1100 μm at 0.1% of peak maximum]. The Kodak plates showed a broader PSF than the Fuji plates, one which also increases with X-ray energy. The standard XRII/CCD gave the coarsest PSF (ca 4000 μm at 0.1% of peak maximum), whereas the finest PSF was recorded with the beryllium XRII/CCD used in magnified mode (900 μm at 0.1%). The best dynamic range was obtained with the XRII/CCDs; the lowest with the Fuji scanner.

Research paper thumbnail of An X-ray Charge-Density Feasibility Study at 56 keV of Magnesium Formate Dihydrate using a CCD Area Detector

Journal of Applied Crystallography, 1997

A high-resolution structural study of magnesium formate dihydrate was performed using high-energy... more A high-resolution structural study of magnesium formate dihydrate was performed using high-energy synchrotron radiation (0.22 A) and an X-ray image intensifier/CCD (charge-coupled device) detector. The complete data collection was performed in less than 2 h. The data were treated by two different integration programs and the results are compared. The data quality was sufficiently high to produce good-quality electron difference density maps.

Research paper thumbnail of Two-dimensional detector software: From real detector to idealised image or two-theta scan

High Pressure Research, 1996

... TWO-DIMENSIONAL DETECTOR SOFTWARE: FROM REAL DETECTOR TO IDEALISED IMAGE OR TWO-THETA SCAN AP... more ... TWO-DIMENSIONAL DETECTOR SOFTWARE: FROM REAL DETECTOR TO IDEALISED IMAGE OR TWO-THETA SCAN AP HAMMERSLEY*, S. 0. SVENSSON, M. HANFLAND, AN FITCH and D. HAUSERMANN ... 235 Page 2. 236 A. P. HAMMERSLEY et al. ...

Research paper thumbnail of Real-time pursuit of diffusionless phase transition in Ni3Sb using synchrotron radiation

Acta Materialia, 1997

Between 5OO'C and 600°C the intermetailic alloy NiSb undergoes a phase transition between a low-t... more Between 5OO'C and 600°C the intermetailic alloy NiSb undergoes a phase transition between a low-temperature orthorhombic phase and a high-temperature cubic phase. We have studied the progress of the phase transition as a function of time by single-crystal diffraction of monochromatic X-rays provided by a synchrotron in combination with a fast read-out CCD based area detector. On cooling and heating it was possible to follow the transition by registering the progressive splitting, respectively the disappearance of the splitting, of the cubic Bragg reflections. in particular (220) and (422). 0 1997 Acta Metallurgica Inc.

Research paper thumbnail of Protein Crystallography at Ultra-Short Wavelengths: Feasibility Study of Anomalous-Dispersion Experiments at the Xenon K-edge

Journal of Synchrotron Radiation, 1997

A protein crystallography experiment at the xenon K-edge (~. = 0.358 A) has been successfully car... more A protein crystallography experiment at the xenon K-edge (~. = 0.358 A) has been successfully carried out at the materials science beamline (BL2/IDll) of the ESRE The samples used in this methodological study were crystals of porcine pancreatic elastase, a 26 kDa protein of known structure. The diffraction data are of excellent quality. The combination of isomorphous replacement and anomalous dispersion of a single xenon heavy-atom derivative allowed accurate phase determination and the computation of a high-quality electron density map of the protein molecule. This is the first fully documented report on a complete protein crystallography experiment, from data collection up to phase determination and calculation of an electron density map, carried out with data obtained at ultra-short wavelengths. Experimental considerations as well as possible advantages and drawbacks of protein crystallography at very short and ultra-short wavelengths are discussed.

Research paper thumbnail of In Situ , Time-Resolved X-ray Diffraction Study of the Solid-State Polymerization of Disulfur Dinitride to Poly(sulfur nitride)

Inorganic Chemistry, 1997

Products and kinetic and mechanistic aspects of the title reaction were investigated by time-reso... more Products and kinetic and mechanistic aspects of the title reaction were investigated by time-resolved X-ray powder diffraction combined with Rietveld refinement. The polymerization of S(2)N(2) at 40 degrees C was monitored with a time resolution better than one diffraction pattern per minute until completion. The reaction product comprised a mixture of monoclinic beta-(SN)(x)() (90%) and an additional orthorhombic phase, identified as alpha-(SN)(x)() (about 10%). The inversely proportional conversion/formation vs time curves for educt and products indicate that the reaction involves only crystalline phases. The cell parameters of polymerizing S(2)N(2) varied noticeably with progressing conversion, whereas the cell volume remained unchanged up to a monomer conversion of 50%. Refinement of atomic coordinates for S and N indicated retention of the reactant geometry. It is concluded that the polymerization of S(2)N(2) to (SN)(x)() is of nondiffusive nature and involves a martensitic transition.

Research paper thumbnail of ISPyB: an information management system for synchrotron macromolecular crystallography

Bioinformatics, 2011

Individual research groups now analyze thousands of samples per year at synchrotron macromolecula... more 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 synchrotronbased 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.

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

Acta crystallographica. Section D, Biological crystallography, 2006

An automatic data-collection system has been implemented and installed on seven insertion-device ... more 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.

Research paper thumbnail of Automation of the collection and processing of X-ray diffraction data – a generic approach

Acta Crystallographica Section D Biological Crystallography, 2002

Research paper thumbnail of Automation of MX data collection and processing

Acta Crystallographica Section A Foundations of Crystallography, 2005

Research paper thumbnail of Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection

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