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1.  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.
The automation of beam delivery, sample handling and data analysis, together with increasing photon flux, diminishing focal spot size and the appearance of fast-readout detectors on synchrotron beamlines, have changed the way that many macromolecular crystallography experiments are planned and executed. Screening for the best diffracting crystal, or even the best diffracting part of a selected crystal, has been enabled by the development of microfocus beams, precise goniometers and fast-readout detectors that all require rapid feedback from the initial processing of images in order to be effective. All of these advances require the coupling of data feedback to the experimental control system and depend on immediate online data-analysis results during the experiment. To facilitate this, a Data Analysis WorkBench (DAWB) for the flexible creation of complex automated protocols has been developed. Here, example workflows designed and implemented using DAWB are presented for enhanced multi-step crystal characterizations, experiments involving crystal re­orientation with kappa goniometers, crystal-burning experiments for empirically determining the radiation sensitivity of a crystal system and the application of mesh scans to find the best location of a crystal to obtain the highest diffraction quality. Beamline users interact with the prepared workflows through a specific brick within the beamline-control GUI MXCuBE.
doi:10.1107/S090744491201863X
PMCID: PMC3413211  PMID: 22868763
workflows; automation; data processing; macromolecular crystallography; experimental protocols; characterization; reorientation; radiation damage
2.  The use of a mini-κ goniometer head in macromolecular crystallography diffraction experiments 
Hardware and software solutions for MX data-collection strategies using the EMBL/ESRF miniaturized multi-axis goniometer head are presented.
Most macromolecular crystallography (MX) diffraction experiments at synchrotrons use a single-axis goniometer. This markedly contrasts with small-molecule crystallography, in which the majority of the diffraction data are collected using multi-axis goniometers. A novel miniaturized κ-gonio­meter head, the MK3, has been developed to allow macromolecular crystals to be aligned. It is available on the majority of the structural biology beamlines at the ESRF, as well as elsewhere. In addition, the Strategy for the Alignment of Crystals (STAC) software package has been developed to facilitate the use of the MK3 and other similar devices. Use of the MK3 and STAC is streamlined by their incorporation into online analysis tools such as EDNA. The current use of STAC and MK3 on the MX beamlines at the ESRF is discussed. It is shown that the alignment of macromolecular crystals can result in improved diffraction data quality compared with data obtained from randomly aligned crystals.
doi:10.1107/S0907444913003880
PMCID: PMC3689527  PMID: 23793150
kappa goniometer; crystal alignment; data-collection strategies
3.  D3, the new diffractometer for the macromolecular crystallography beamlines of the Swiss Light Source 
Journal of Synchrotron Radiation  2014;21(Pt 2):340-351.
A new diffractometer for microcrystallography has been developed for the three macromolecular crystallography beamlines of the Swiss Light Source.
A new diffractometer for microcrystallography has been developed for the three macromolecular crystallography beamlines of the Swiss Light Source. Building upon and critically extending previous developments realised for the high-resolution endstations of the two undulator beamlines X06SA and X10SA, as well as the super-bend dipole beamline X06DA, the new diffractometer was designed to the following core design goals. (i) Redesign of the goniometer to a sub-micrometer peak-to-peak cylinder of confusion for the horizontal single axis. Crystal sizes down to at least 5 µm and advanced sample-rastering and scanning modes are supported. In addition, it can accommodate the new multi-axis goniometer PRIGo (Parallel Robotics Inspired Goniometer). (ii) A rapid-change beam-shaping element system with aperture sizes down to a minimum of 10 µm for microcrystallography measurements. (iii) Integration of the on-axis microspectrophotometer MS3 for microscopic sample imaging with 1 µm image resolution. Its multi-mode optical spectroscopy module is always online and supports in situ UV/Vis absorption, fluorescence and Raman spectroscopy. (iv) High stability of the sample environment by a mineral cast support construction and by close containment of the cryo-stream. Further features are the support for in situ crystallization plate screening and a minimal achievable detector distance of 120 mm for the Pilatus 6M, 2M and the macromolecular crystallography group’s planned future area detector Eiger 16M.
doi:10.1107/S160057751400006X
PMCID: PMC3945418  PMID: 24562555
macromolecular crystallography; diffractometer; microspectrophotometer; microcrystallography; beamline endstation
4.  Objective assessment, repeatability, and agreement of shoulder ROM with a 3D gyroscope 
Background
Assessment of shoulder mobility is essential for diagnosis and clinical follow-up of shoulder diseases. Only a few highly sophisticated instruments for objective measurements of shoulder mobility are available. The recently introduced DynaPort MiniMod TriGyro ShoulderTest-System (DP) was validated earlier in laboratory trials. We aimed to assess the precision (repeatability) and agreement of this instrument in human subjects, as compared to the conventional goniometer.
Methods
The DP is a small, light-weight, three-dimensional gyroscope that can be fixed on the distal upper arm, recording shoulder abduction, flexion, and rotation. Twenty-one subjects (42 shoulders) were included for analysis. Two subsequent assessments of the same subject with a 30-minute delay in testing of each shoulder were performed with the DP in two directions (flexion and abduction), and simultaneously correlated with the measurements of a conventional goniometer. All assessments were performed by one observer. Repeatability for each method was determined and compared as the statistical variance between two repeated measurements. Agreement was illustrated by Bland-Altman-Plots with 95% limits of agreement. Statistical analysis was performed with a linear mixed regression model. Variance for repeated measurements by the same method was also estimated and compared with the likelihood-ratio test.
Results
Evaluation of abduction showed significantly better repeatability for the DP compared to the conventional goniometer (error variance: DP = 0.89, goniometer = 8.58, p = 0.025). No significant differences were found for flexion (DP = 1.52, goniometer = 5.94, p = 0.09). Agreement assessment was performed for flexion for mean differences of 0.27° with 95% limit of agreement ranging from −7.97° to 8.51°. For abduction, the mean differences were 1.19° with a 95% limit of agreement ranging from −9.07° to 11.46°.
Conclusion
In summary, DP demonstrated a high precision even higher than the conventional goniometer. Agreement between both methods is acceptable, with possible deviations of up to greater than 10°. Therefore, static measurements with DP are more precise than conventional goniometer measurements. These results are promising for routine clinical use of the DP.
doi:10.1186/1471-2474-14-72
PMCID: PMC3614536  PMID: 23442604
Repeatability; Precision; Shoulder motion; Objective assessment; Dynaport; Gyroscope
5.  A decade of user operation on the macromolecular crystallography MAD beamline ID14-4 at the ESRF 
Journal of Synchrotron Radiation  2009;16(Pt 6):803-812.
The improvement of the X-ray beam quality achieved on ID14-4 by the installation of new X-ray optical elements is described.
ID14-4 at the ESRF is the first tunable undulator-based macromolecular crystallography beamline that can celebrate a decade of user service. During this time ID14-4 has not only been instrumental in the determination of the structures of biologically important molecules but has also contributed significantly to the development of various instruments, novel data collection schemes and pioneering radiation damage studies on biological samples. Here, the evolution of ID14-4 over the last decade is presented, and some of the major improvements that were carried out in order to maintain its status as one of the most productive macromolecular crystallography beamlines are highlighted. The experimental hutch has been upgraded to accommodate a high-precision diffractometer, a sample changer and a large CCD detector. More recently, the optical hutch has been refurbished in order to improve the X-ray beam quality on ID14-4 and to incorporate the most modern and robust optical elements used at other ESRF beamlines. These new optical elements will be described and their effect on beam stability discussed. These studies may be useful in the design, construction and maintenance of future X-ray beamlines for macromolecular crystallography and indeed other applications, such as those planned for the ESRF upgrade.
doi:10.1107/S0909049509035377
PMCID: PMC2765085  PMID: 19844017
macromolecular crystallography; X-ray beam quality; beamline diagnostics; beamline automation
6.  How the ESRF helps industry and how they help the ESRF 
The key features of the functionality facilitating proprietary use of the ESRF’s structural biology beamlines are described, as are the major advantages, in terms of beamline evolution, of the interaction of the ESRF with the pharmaceutical industry.
The ESRF has worked with, and provided services for, the pharmaceutical industry since the construction of its first protein crystallography beamline in the mid-1990s. In more recent times, industrial clients have benefited from a portfolio of beamlines which offer a wide range of functionality and beam characteristics, including tunability, microfocus and micro-aperture. Included in this portfolio is a small-angle X-­ray scattering beamline dedicated to the study of biological molecules in solution. The high demands on throughput and efficiency made by the ESRF’s industrial clients have been a major driving force in the evolution of the ESRF’s macromolecular crystallography resources, which now include remote access, the automation of crystal screening and data collection, and a beamline database allowing sample tracking, experiment reporting and real-time at-a-distance monitoring of experiments. This paper describes the key features of the functionality put in place on the ESRF structural biology beamlines and outlines the major advantages of the interaction of the ESRF with the pharmaceutical industry.
doi:10.1107/S0907444913001108
PMCID: PMC3689532  PMID: 23793155
synchrotron MX beamlines; proprietary access; service data collection; automation
7.  Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF 
Journal of Applied Crystallography  2013;46(Pt 3):804-810.
A system for the automatic reduction of single- and multi-position macromolecular crystallography data is presented.
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 single or multiple crystals has been developed. Standard integration and data analysis programs have been incorporated into the ESRF data collection, storage and computing environment, with the final results stored and displayed in an intuitive manner in the ISPyB (information system for protein crystallography beamlines) database, from which they are also available for download. In some cases, experimental phase information can be automatically determined from the processed data. Here, the system is described in detail.
doi:10.1107/S0021889813006195
PMCID: PMC3654316  PMID: 23682196
automation; data processing; macromolecular crystallography; computer programs
8.  Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin 
Journal of Synchrotron Radiation  2012;19(Pt 3):442-449.
The three macromolecular crystallography beamlines BL14.1, BL14.2 and BL14.3 at the BESSY II storage ring at the Helmholtz-Zentrum Berlin are described.
Three macromolecular crystallography (MX) beamlines at the Helmholtz-Zentrum Berlin (HZB) are available for the regional, national and international structural biology user community. The state-of-the-art synchrotron beamlines for MX BL14.1, BL14.2 and BL14.3 are located within the low-β section of the BESSY II electron storage ring. All beamlines are fed from a superconducting 7 T wavelength-shifter insertion device. BL14.1 and BL14.2 are energy tunable in the range 5–16 keV, while BL14.3 is a fixed-energy side station operated at 13.8 keV. All three beamlines are equipped with CCD detectors. BL14.1 and BL14.2 are in regular user operation providing about 200 beam days per year and about 600 user shifts to approximately 50 research groups across Europe. BL14.3 has initially been used as a test facility and was brought into regular user mode operation during the year 2010. BL14.1 has recently been upgraded with a microdiffractometer including a mini-κ goniometer and an automated sample changer. Additional user facilities include office space adjacent to the beamlines, a sample preparation laboratory, a biology laboratory (safety level 1) and high-end computing resources. In this article the instrumentation of the beamlines is described, and a summary of the experimental possibilities of the beamlines and the provided ancillary equipment for the user community is given.
doi:10.1107/S0909049512006395
PMCID: PMC3408958  PMID: 22514183
macromolecular crystallography beamlines; high-throughput methods; crystal dehydration; UV radiation-damage-induced phasing; long-wavelength phasing
9.  Developments in optics and performance at BL13-XALOC, the macromolecular crystallography beamline at the Alba Synchrotron 
Journal of Synchrotron Radiation  2014;21(Pt 4):679-689.
The design, performance and first results of the new macromolecular crystallography beamline BL13-XALOC at the ALBA Synchrotron are described, including new developments in optics and control.
BL13-XALOC is currently the only macromolecular crystallography beamline at the 3 GeV ALBA synchrotron near Barcelona, Spain. The optics design is based on an in-vacuum undulator, a Si(111) channel-cut crystal monochromator and a pair of KB mirrors. It allows three main operation modes: a focused configuration, where both mirrors can focus the beam at the sample position to 52 µm × 5.5 µm FWHM (H × V); a defocused configuration that can match the size of the beam to the dimensions of the crystals or to focus the beam at the detector; and an unfocused configuration, where one or both mirrors are removed from the photon beam path. To achieve a uniform defocused beam, the slope errors of the mirrors were reduced down to 55 nrad RMS by employing a novel method that has been developed at the ALBA high-accuracy metrology laboratory. Thorough commissioning with X-ray beam and user operation has demonstrated an excellent energy and spatial stability of the beamline. The end-station includes a high-accuracy single-axis diffractometer, a removable mini-kappa stage, an automated sample-mounting robot and a photon-counting detector that allows shutterless operation. The positioning tables of the diffractometer and the detector are based on a novel and highly stable design. This equipment, together with the operation flexibility of the beamline, allows a large variety of types of crystals to be tackled, from medium-sized crystals with large unit-cell parameters to microcrystals. Several examples of data collections measured during beamline commissioning are described. The beamline started user operation on 18 July 2012.
doi:10.1107/S160057751400825X
PMCID: PMC4073956  PMID: 24971961
macromolecular crystallography; beamline; Alba; mirror slope errors
10.  Mini-beam collimator enables microcrystallography experiments on standard beamlines 
Journal of Synchrotron Radiation  2009;16(Pt 2):217-225.
A ‘mini-beam’ apparatus has been developed that conditions the size of an X-ray beam to 5 µm. The design of the apparatus and the characterization of the focal size and flux are presented.
The high-brilliance X-ray beams from undulator sources at third-generation synchrotron facilities are excellent tools for solving crystal structures of important and challenging biological macromolecules and complexes. However, many of the most important structural targets yield crystals that are too small or too inhomogeneous for a ‘standard’ beam from an undulator source, ∼25–50 µm (FWHM) in the vertical and 50–100 µm in the horizontal direction. Although many synchrotron facilities have microfocus beamlines for other applications, this capability for macromolecular crystallography was pioneered at ID-13 of the ESRF. The National Institute of General Medical Sciences and National Cancer Institute Collaborative Access Team (GM/CA-CAT) dual canted undulator beamlines at the APS deliver high-intensity focused beams with a minimum focal size of 20 µm × 65 µm at the sample position. To meet growing user demand for beams to study samples of 10 µm or less, a ‘mini-beam’ apparatus was developed that conditions the focused beam to either 5 µm or 10 µm (FWHM) diameter with high intensity. The mini-beam has a symmetric Gaussian shape in both the horizontal and vertical directions, and reduces the vertical divergence of the focused beam by 25%. Significant reduction in background was achieved by implementation of both forward- and back-scatter guards. A unique triple-collimator apparatus, which has been in routine use on both undulator beamlines since February 2008, allows users to rapidly interchange the focused beam and conditioned mini-beams of two sizes with a single mouse click. The device and the beam are stable over many hours of routine operation. The rapid-exchange capability has greatly facilitated sample screening and resulted in several structures that could not have been obtained with the larger focused beam.
doi:10.1107/S0909049508040612
PMCID: PMC2725011  PMID: 19240333
mini-beam; microbeam; microdiffraction; macromolecular crystallography
11.  X-ray diffractometry for the structure determination of a submicrometre single powder grain 
Journal of Synchrotron Radiation  2009;16(Pt 3):352-357.
A high-precision diffractometer with a synchrotron radiation microfocusing technique has been developed to investigate the crystal structure of a submicrometre-scale single grain of powder sample. The structure of a BaTiO3 single powder grain, of dimensions ∼600 × 600 × 300 nm, was determined.
A high-precision diffractometer has been developed for the structure analysis of a submicrometre-scale single grain of a powder sample at the SPring-8 BL40XU undulator beamline. The key design concept is the combination of a stable focused synchrotron radiation beam and the precise axis control of the diffractometer, which allows accurate diffraction intensity data of a submicrometre-scale single powder grain to be measured. The phase zone plate was designed to create a high-flux focused synchrotron radiation beam. A low-eccentric goniometer and high-precision sample positioning stages were adopted to ensure the alignment of a micrometre-scale focused synchrotron radiation beam onto the submicrometre-scale single powder grain. In order to verify the diffractometer performance, the diffraction pattern data of several powder grains of BaTiO3, of dimensions ∼600 × 600 × 300 nm, were measured. By identifying the diffraction data set of one single powder grain, the crystal structure was successfully determined with a reliable factor of 5.24%.
doi:10.1107/S090904950900675X
PMCID: PMC2678016  PMID: 19395798
submicrometre X-ray beam; phase zone plate; X-ray diffraction; single-crystal structure analysis; powder diffraction
12.  MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments 
Journal of Synchrotron Radiation  2010;17(Pt 5):700-707.
MxCuBE is a beamline control environment optimized for the needs of macromolecular crystallography. This paper describes the design of the software and the features that MxCuBE currently provides.
The design and features of a beamline control software system for macromolecular crystallography (MX) experiments developed at the European Synchrotron Radiation Facility (ESRF) are described. This system, MxCuBE, allows users to easily and simply interact with beamline hardware components and provides automated routines for common tasks in the operation of a synchrotron beamline dedicated to experiments in MX. Additional functionality is provided through intuitive interfaces that enable the assessment of the diffraction characteristics of samples, experiment planning, automatic data collection and the on-line collection and analysis of X-ray emission spectra. The software can be run in a tandem client-server mode that allows for remote control and relevant experimental parameters and results are automatically logged in a relational database, ISPyB. MxCuBE is modular, flexible and extensible and is currently deployed on eight macromolecular crystallography beamlines at the ESRF. Additionally, the software is installed at MAX-lab beamline I911-3 and at BESSY beamline BL14.1.
doi:10.1107/S0909049510020005
PMCID: PMC3025540  PMID: 20724792
automation; macromolecular crystallography; synchrotron beamline control; graphical user interface
13.  The ID23-2 structural biology microfocus beamline at the ESRF 
Journal of Synchrotron Radiation  2009;17(Pt 1):107-118.
Beamline ID23-2, the first dedicated and highly automated high-throughput monochromatic macromolecular crystallography microfocus beamline, is described.
The first phase of the ESRF beamline ID23 to be constructed was ID23-1, a tunable MAD-capable beamline which opened to users in early 2004. The second phase of the beamline to be constructed is ID23-2, a monochromatic microfocus beamline dedicated to macromolecular crystallography experiments. Beamline ID23-2 makes use of well characterized optical elements: a single-bounce silicon (111) monochromator and two mirrors in Kirkpatrick–Baez geometry to focus the X-ray beam. A major design goal of the ID23-2 beamline is to provide a reliable, easy-to-use and routine microfocus beam. ID23-2 started operation in November 2005, as the first beamline dedicated to microfocus macromolecular crystallography. The beamline has taken the standard automated ESRF macromolecular crystallography environment (both hardware and software), allowing users of ID23-2 to be rapidly familiar with the microfocus environment. This paper describes the beamline design, the special considerations taken into account given the microfocus beam, and summarizes the results of the first years of the beamline operation.
doi:10.1107/S0909049509041168
PMCID: PMC3025444  PMID: 20029119
macromolecular crystallography; automation; microfocus
14.  Experimental procedure for the characterization of radiation damage in macromolecular crystals 
Journal of Synchrotron Radiation  2011;18(Pt 3):381-386.
A novel automatic procedure to determine the sensitivity of macromolecular crystals to radiation damage is presented. The information extracted from this procedure can be directly used for optimal planning of data collection or/and beamline calibration.
A reliable and reproducible method to automatically characterize the radiation sensitivity of macromolecular crystals at the ESRF beamlines has been developed. This new approach uses the slope of the linear dependence of the overall isotropic B-factor with absorbed dose as the damage metric. The method has been implemented through an automated procedure using the EDNA on-line data analysis framework and the MxCuBE data collection control interface. The outcome of the procedure can be directly used to design an optimal data collection strategy. The results of tests carried out on a number of model and real-life crystal systems are presented.
doi:10.1107/S0909049511002251
PMCID: PMC3268693  PMID: 21525646
BEST; EDNA; radiation damage
15.  Wearable Conductive Fiber Sensors for Multi-Axis Human Joint Angle Measurements 
Background
The practice of continuous, long-term monitoring of human joint motion is one that finds many applications, especially in the medical and rehabilitation fields. There is a lack of acceptable devices available to perform such measurements in the field in a reliable and non-intrusive way over a long period of time. The purpose of this study was therefore to develop such a wearable joint monitoring sensor capable of continuous, day-to-day monitoring.
Methods
A novel technique of incorporating conductive fibers into flexible, skin-tight fabrics surrounding a joint is developed. Resistance changes across these conductive fibers are measured, and directly related to specific single or multi-axis joint angles through the use of a non-linear predictor after an initial, one-time calibration. Because these sensors are intended for multiple uses, an automated registration algorithm has been devised using a sensitivity template matched to an array of sensors spanning the joints of interest. In this way, a sensor array can be taken off and put back on an individual for multiple uses, with the sensors automatically calibrating themselves each time.
Results
The wearable sensors designed are comfortable, and acceptable for long-term wear in everyday settings. Results have shown the feasibility of this type of sensor, with accurate measurements of joint motion for both a single-axis knee joint and a double axis hip joint when compared to a standard goniometer used to measure joint angles. Self-registration of the sensors was found to be possible with only a few simple motions by the patient.
Conclusion
After preliminary experiments involving a pants sensing garment for lower body monitoring, it has been seen that this methodology is effective for monitoring joint motion of the hip and knee. This design therefore produces a robust, comfortable, truly wearable joint monitoring device.
doi:10.1186/1743-0003-2-7
PMCID: PMC555561  PMID: 15740632
16.  New generation of wearable goniometers for motion capture systems 
Background
Monitoring joint angles through wearable systems enables human posture and gesture to be reconstructed as a support for physical rehabilitation both in clinics and at the patient’s home. A new generation of wearable goniometers based on knitted piezoresistive fabric (KPF) technology is presented.
Methods
KPF single-and double-layer devices were designed and characterized under stretching and bending to work as strain sensors and goniometers. The theoretical working principle and the derived electromechanical model, previously proved for carbon elastomer sensors, were generalized to KPF. The devices were used to correlate angles and piezoresistive fabric behaviour, to highlight the differences in terms of performance between the single layer and the double layer sensors. A fast calibration procedure is also proposed.
Results
The proposed device was tested both in static and dynamic conditions in comparison with standard electrogoniometers and inertial measurement units respectively. KPF goniometer capabilities in angle detection were experimentally proved and a discussion of the device measurement errors of is provided. The paper concludes with an analysis of sensor accuracy and hysteresis reduction in particular configurations.
Conclusions
Double layer KPF goniometers showed a promising performance in terms of angle measurements both in quasi-static and dynamic working mode for velocities typical of human movement. A further approach consisting of a combination of multiple sensors to increase accuracy via sensor fusion technique has been presented.
doi:10.1186/1743-0003-11-56
PMCID: PMC3996949  PMID: 24725669
17.  AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery 
New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples.
AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallo­graphy steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data, performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully demonstrated. This workflow was run once on the same 96 samples that the group had examined manually and the workflow cycled successfully through all of the samples, collected data from the same samples that were selected manually and located the same peaks of unmodeled density in the resulting difference Fourier maps.
doi:10.1107/S0907444913001984
PMCID: PMC3640469  PMID: 23633588
AutoDrug; fragment-based drug discovery; workflow automation
18.  High-throughput operation of sample-exchange robots with double tongs at the Photon Factory beamlines 
Journal of Synchrotron Radiation  2008;15(Pt 3):300-303.
Sample-exchange robots with a double-tongs system that could exchange samples within 10 s have been developed.
Sample-exchange robots that can exchange cryo-pins bearing protein crystals out of experimental hutches according to user instructions have been developed. The robots were designed based on the SAM (Stanford Synchrotron Research Laboratory automated mounting) system. In order to reduce the time required for the sample exchange, the single tongs of the SAM system were modified and a double-tongs system that can hold two cryo-pins at the same time was developed. Robots with double tongs can move to the goniometer head holding the next cryo-pin with one set of tongs, dismount the experimented cryo-pin with the other set, and then mount the next pin onto the goniometer head without leaving the diffractometer area. Two different types of tongs have been installed: single tongs at beamlines BL-5A and AR-NW12A, and a double-tongs system at beamline BL-17A of the Photon Factory. The same graphical user interface software for operation of the sample-exchange robots is used at all beamlines, however, so that users do not need to consider differences between the systems. In a trial, the robot with double tongs could exchange samples within 10 s.
doi:10.1107/S0909049507064680
PMCID: PMC2394784  PMID: 18421164
sample-exchange robot; protein crystallography; automated system; diffraction experiment
19.  Reliability of goniometric measurements in children with cerebral palsy: A comparative analysis of universal goniometer and electronic inclinometer. A pilot study 
Background
Even though technological progress has provided us with more and more sophisticated equipment for making goniometric measurements, the most commonly used clinical tools are still the universal goniometer and, to a lesser extent, the inclinometer. There is, however, no published study so far that uses an inclinometer for measurements in children with cerebral palsy (CP). The objective of this study was two-fold: to independently assess the intra and inter-examiner reliability for measuring the hip abduction range of motion in children with CP using two different instruments, the universal two-axis goniometer and electronic inclinometer. A pool of 5 examiners with different levels of experience as paediatric physiotherapists participated. The study did not compare both instruments because the measurement procedure and the hip position were different for each.
Methods
A prospective, observational study of goniometery was carried out with 14 lower extremities of 7 children with spastic CP. The inclinometer study was carried out with 8 lower extremities of 4 children with spastic CP. This study was divided into two independent parts: a study of the reliability of the hip abduction range of motion measured with a universal goniometer (hip at 0° flexion) and with an electronic inclinometer (hip at 90° flexion). The Intraclass Correlation Coefficient (ICC) was calculated to analyse intra and inter-examiner agreement for each instrument.
Results
For the goniometer, the intra-examiner reliability was excellent (>0.80), while the inter-examiner reliability was low (0.375 and 0.475). For the inclinometer, both the intra-examiner (0.850-0.975) and inter-examiner reliability were excellent (0.965 and 0.979).
Conclusions
The inter-examiner reliability for goniometric measurement of hip abduction in children with CP was low, in keeping with other results found in previous publications. The inclinometer has proved to be a highly reliable tool for measuring the hip abduction range of motion in children with CP, which opens up new possibilities in this field, despite having some measurement limitations.
doi:10.1186/1471-2474-12-155
PMCID: PMC3160434  PMID: 21740600
20.  In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF 
The current version of the Cryobench in crystallo optical spectroscopy facility of the ESRF is presented. The diverse experiments that can be performed at the Cryobench are also reviewed.
The analysis of structural data obtained by X-ray crystallo­graphy benefits from information obtained from complementary techniques, especially as applied to the crystals themselves. As a consequence, optical spectroscopies in structural biology have become instrumental in assessing the relevance and context of many crystallographic results. Since the year 2000, it has been possible to record such data adjacent to, or directly on, the Structural Biology Group beamlines of the ESRF. A core laboratory featuring various spectrometers, named the Cryobench, is now in its third version and houses portable devices that can be directly mounted on beamlines. This paper reports the current status of the Cryobench, which is now located on the MAD beamline ID29 and is thus called the ID29S-Cryobench (where S stands for ‘spectroscopy’). It also reviews the diverse experiments that can be performed at the Cryobench, highlighting the various scientific questions that can be addressed.
doi:10.1107/S139900471401517X
PMCID: PMC4304682  PMID: 25615856
in crystallo optical spectroscopy; Cryobench; UV-visible light absorption spectroscopy; fluorescence spectroscopy; Raman spectroscopy
21.  Improvement of an automated protein crystal exchange system PAM for high-throughput data collection 
Journal of Synchrotron Radiation  2013;20(Pt 6):890-893.
A special liquid-nitrogen Dewar with double capacity for the sample-exchange robot has been created at AR-NE3A at the Photon Factory, allowing continuous fully automated data collection. In this work, this new system is described and the stability of its calibration is discussed.
Photon Factory Automated Mounting system (PAM) protein crystal exchange systems are available at the following Photon Factory macromolecular beamlines: BL-1A, BL-5A, BL-17A, AR-NW12A and AR-NE3A. The beamline AR-NE3A has been constructed for high-throughput macromolecular crystallography and is dedicated to structure-based drug design. The PAM liquid-nitrogen Dewar can store a maximum of three SSRL cassettes. Therefore, users have to interrupt their experiments and replace the cassettes when using four or more of them during their beam time. As a result of investigation, four or more cassettes were used in AR-NE3A alone. For continuous automated data collection, the size of the liquid-nitrogen Dewar for the AR-NE3A PAM was increased, doubling the capacity. In order to check the calibration with the new Dewar and the cassette stand, calibration experiments were repeatedly performed. Compared with the current system, the parameters of the novel system are shown to be stable.
doi:10.1107/S0909049513021067
PMCID: PMC3795550  PMID: 24121334
protein crystallography; sample-exchange robot; automated system
22.  Reliability of the standard goniometry and diagrammatic recording of finger joint angles: a comparative study with healthy subjects and non-professional raters 
Background
Diagrammatic recording of finger joint angles by using two criss-crossed paper strips can be a quick substitute to the standard goniometry. As a preliminary step toward clinical validation of the diagrammatic technique, the current study employed healthy subjects and non-professional raters to explore whether reliability estimates of the diagrammatic goniometry are comparable with those of the standard procedure.
Methods
The study included two procedurally different parts, which were replicated by assigning 24 medical students to act interchangeably as 12 subjects and 12 raters. A larger component of the study was designed to compare goniometers side-by-side in measurement of finger joint angles varying from subject to subject. In the rest of the study, the instruments were compared by parallel evaluations of joint angles similar for all subjects in a situation of simulated change of joint range of motion over time. The subjects used special guides to position the joints of their left ring finger at varying angles of flexion and extension. The obtained diagrams of joint angles were converted to numerical values by computerized measurements. The statistical approaches included calculation of appropriate intraclass correlation coefficients, standard errors of measurements, proportions of measurement differences of 5 or less degrees, and significant differences between paired observations.
Results
Reliability estimates were similar for both goniometers. Intra-rater and inter-rater intraclass correlation coefficients ranged from 0.69 to 0.93. The corresponding standard errors of measurements ranged from 2.4 to 4.9 degrees. Repeated measurements of a considerable number of raters fell within clinically non-meaningful 5 degrees of each other in proportions comparable with a criterion value of 0.95. Data collected with both instruments could be similarly interpreted in a simulated situation of change of joint range of motion over time.
Conclusions
The paper goniometer and the standard goniometer can be used interchangeably by non-professional raters for evaluation of normal finger joints. The obtained results warrant further research to assess clinical performance of the paper strip technique.
doi:10.1186/1471-2474-14-17
PMCID: PMC3557198  PMID: 23302419
23.  A Manual Transportable Instrument Platform for Ground-Based Spectro-Directional Observations (ManTIS) and the Resultant Hyperspectral Field Goniometer System 
Sensors (Basel, Switzerland)  2013;13(12):16105-16128.
This article presents and technically describes a new field spectro-goniometer system for the ground-based characterization of the surface reflectance anisotropy under natural illumination conditions developed at the Alfred Wegener Institute (AWI). The spectro-goniometer consists of a Manual Transportable Instrument platform for ground-based Spectro-directional observations (ManTIS), and a hyperspectral sensor system. The presented measurement strategy shows that the AWI ManTIS field spectro-goniometer can deliver high quality hemispherical conical reflectance factor (HCRF) measurements with a pointing accuracy of ±6 cm within the constant observation center. The sampling of a ManTIS hemisphere (up to 30° viewing zenith, 360° viewing azimuth) needs approx. 18 min. The developed data processing chain in combination with the software used for the semi-automatic control provides a reliable method to reduce temporal effects during the measurements. The presented visualization and analysis approaches of the HCRF data of an Arctic low growing vegetation showcase prove the high quality of spectro-goniometer measurements. The patented low-cost and lightweight ManTIS instrument platform can be customized for various research needs and is available for purchase.
doi:10.3390/s131216105
PMCID: PMC3892848
reflectance anisotropy; spectro-directional remote sensing; spectro-goniometer; HDRF; BRDF; hyperspectral HCRF measurements
24.  Three-dimensional rotation electron diffraction: software RED for automated data collection and data processing 
Journal of Applied Crystallography  2013;46(Pt 6):1863-1873.
Implementation of the RED software package for automated collection and processing of rotation electron diffraction data is described.
Implementation of a computer program package for automated collection and processing of rotation electron diffraction (RED) data is described. The software package contains two computer programs: RED data collection and RED data processing. The RED data collection program controls the transmission electron microscope and the camera. Electron beam tilts at a fine step (0.05–0.20°) are combined with goniometer tilts at a coarse step (2.0–3.0°) around a common tilt axis, which allows a fine relative tilt to be achieved between the electron beam and the crystal in a large tilt range. An electron diffraction (ED) frame is collected at each combination of beam tilt and goniometer tilt. The RED data processing program processes three-dimensional ED data generated by the RED data collection program or by other approaches. It includes shift correction of the ED frames, peak hunting for diffraction spots in individual ED frames and identification of these diffraction spots as reflections in three dimensions. Unit-cell parameters are determined from the positions of reflections in three-dimensional reciprocal space. All reflections are indexed, and finally a list with hkl indices and intensities is output. The data processing program also includes a visualizer to view and analyse three-dimensional reciprocal lattices reconstructed from the ED frames. Details of the implementation are described. Data collection and data processing with the software RED are demonstrated using a calcined zeolite sample, silicalite-1. The structure of the calcined silicalite-1, with 72 unique atoms, could be solved from the RED data by routine direct methods.
doi:10.1107/S0021889813027714
PMCID: PMC3831301  PMID: 24282334
rotation electron diffraction; electron diffraction tomography; three-dimensional electron diffraction; structure analysis; electron diffraction; computer programs
25.  Acoustic methods for high-throughput protein crystal mounting at next-generation macromolecular crystallographic beamlines 
Journal of Synchrotron Radiation  2013;20(Pt 5):805-808.
A new system has been developed and tested at the National Synchrotron Light Source with the goal of enabling rapid protein crystal mounting at next-generation macromolecular crystallographic beamlines. The system uses an acoustic ejector to deposit nanoliter-volume droplets containing crystals onto an X-ray transparent conveyor belt, which then moves the droplets into position for cryo-cooling and data collection. The acoustic ejector is capable of operating at a rate of several hundred droplet ejections per second.
To take full advantage of advanced data collection techniques and high beam flux at next-generation macromolecular crystallography beamlines, rapid and reliable methods will be needed to mount and align many samples per second. One approach is to use an acoustic ejector to eject crystal-containing droplets onto a solid X-ray transparent surface, which can then be positioned and rotated for data collection. Proof-of-concept experiments were conducted at the National Synchrotron Light Source on thermolysin crystals acoustically ejected onto a polyimide ‘conveyor belt’. Small wedges of data were collected on each crystal, and a complete dataset was assembled from a well diffracting subset of these crystals. Future developments and implementation will focus on achieving ejection and translation of single droplets at a rate of over one hundred per second.
doi:10.1107/S0909049513020372
PMCID: PMC3747951  PMID: 23955046
acoustic droplet ejection; conveyor belt; crystal mounting; high throughput; X-ray diffraction; macromolecular crystallography

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