Beamline Users Research Articles

Data Management System at the Photon Factory Macromolecular Crystallography Beamline

Macromolecular crystallography is a very powerful tool to investigate three-dimensional structures of macromolecules at the atomic level, and is widely spread among structural biology researchers. Due to recent upgrades of the macromolecular crystallography beamlines at the Photon Factory, beamline throughput has improved, allowing more experiments to be conducted during a user's beam time. Although the number of beamlines has increased, so has the number of beam time applications. Consequently, both the experimental data from users' experiments and data derived from beamline operations have dramatically increased, causing difficulties in organizing these diverse and large amounts of data for the beamline operation staff and users. To overcome this problem, we have developed a data management system by introducing commercial middleware, which consists of a controller, database, and web servers. We have prepared several database projects using this system. Each project is dedicated to a certain aspect such as experimental results, beam time applications, beam time schedule, or beamline operation reports. Then we designed a scheme to link all the database projects.

X-ray absorption spectroscopy at a protein crystallography facility: the Canadian Light Source beamline 08B1-1

It is now possible to perform X-ray absorption spectroscopy (XAS) on metalloprotein crystals at the Canadian Macromolecular Crystallography Facility bend magnet (CMCF-BM) beamline (08B1-1) at the Canadian Light Source. The recent addition of a four-element fluorescence detector allows users to acquire data suitable for X-ray absorption near-edge structure and extended X-ray absorption fine-structure based studies by monitoring fluorescence. CMCF beamline users who wish to supplement their diffraction data with XAS can do so with virtually no additional sample preparation. XAS data collection is integrated with the established Mx Data Collector software package used to collect diffraction data. Mainstream XAS data-processing software packages are available for the users; assistance with data processing and interpretation by staff is also available upon request.

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

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.

Magnetic Design of the Advanced Light Source Harmonic Sextupoles

Forty-eight harmonic sextupole magnets with integrated dipole correctors and skew quadrupole coils will be introduced in the Advanced Light Source Storage Ring. These new magnets are required to allow the ALS to provide the 40 beamline users with higher photon beam brightness (factor of 2 or 3). Introducing new combined-function magnets in an existing storage ring is a challenge due to the limited space available and a balance had to be found between magnet performance and spatial constraints. Consequently four different magnet designs were required. The calculation and simulation results obtained for each design as well as the impact of the different design choices on the magnetic performance are developed in this paper.

Neutron Instruments at J-PARC: Toward the State-of-the-Art Facility

Since 2001, researchers, engineers and other members in the MLF (Materials and Life Science) division have not only intensively constructed instruments, but they have also been involved in facility management, including process control of beamline construction, safety, maintenance, user support, beamtime management, outreach, and development of the proposal system. Although the beam power achieved by the end of 2009 was only 1/10 of the designed value, it has reached 40 times the power of KENS's beam power. The repetition rate of 25 Hz, which is much smaller than that of the first target station at ISIS (50 Hz) and SNS (60 Hz), highlights the uniqueness of the neutron instruments at JPARC, where a wide dynamical range is attained with limited loss of neutrons.

Synchrotron radiation circular dichroism (SRCD) spectroscopy: An emerging method in structural biology for examining protein conformations and protein interactions

Circular dichroism (CD) spectroscopy is a well-established technique in structural biology. The use of synchrotron radiation as an intense light source for these measurements extends the applications possible using lab-based instruments. In recent years, there has been a major growth in synchrotron radiation circular dichroism (SRCD) beamlines worldwide, including ones at the NSLS, ISA, SRS, HiSOR, BSRF, NSRRC, SOLEIL, Diamond, TERAS, BESSYII, and ANKA synchrotrons. Through the coordinated efforts of beamline scientists and users at these sites, important proof-of-principle studies have been done enabling the method to be developed for novel and productive studies on biological systems. This paper describes the characteristics of SRCD beamlines and some of the new types of applications that have been undertaken using these beamlines.

Mail-in data collection at SPring-8 protein crystallography beamlines

A mail-in data collection system makes it possible for beamline users to collect diffraction data without visiting a synchrotron facility. In the mail-in data collection system at SPring-8, users pack crystals into sample trays and send the trays to SPring-8 via a courier service as the first step. Next, the user specifies measurement conditions and checks the diffraction images via the Internet. The user can also collect diffraction data using an automated sample changer robot and beamline control software. For distant users there is a newly developed data management system, D-Cha. D-Cha provides a graphical user interface that enables the user to specify the experimental conditions for samples and to check and download the diffraction images using a web browser. This system is now in routine operation and is contributing to high-throughput beamline operation.

Mail-in data collection at SPring-8 protein crystallography beamlines

A mail-in data collection system makes it possible for beamline users to collect diffraction data without visiting a synchrotron facility. In the mail-in data collection system at SPring-8, users pack crystals into sample trays and send the trays to SPring-8 via a courier service as the first step. Next, the user specifies measurement conditions and checks the diffraction images via the Internet. The user can also collect diffraction data using an automated sample changer robot and beamline control software. For distant users there is a newly developed data management system, D-Cha. D-Cha provides a graphical user interface that enables the user to specify the experimental conditions for samples and to check and download the diffraction images using a web browser. This system is now in routine operation and is contributing to high-throughput beamline operation.

The Canadian Light Source: The newest synchrotron in the Americas

The Canadian Light Source (CLS) is a 2.9 GeV synchrotron facility. It consists of seven user beamlines (not including two facility diagnostic beamlines), seven more under construction, and five additional beamlines for which funding has been announced. This article describes some details of the initial stages of operation.

The ID23-1 structural biology beamline at the ESRF

The demand for access to macromolecular crystallography synchrotron beam time continues to increase. To meet this demand the ESRF has constructed a dual station beamline using a canted undulator system as the X-ray source. The first phase of the beamline to be constructed is ID23-1, a tunable MAD-capable station with a mini-focus X-ray beam. The beamline makes use of well characterized optical elements: a channel-cut monochromator with a high-precision toroidal mirror to focus the X-ray beam. The beamline has been conceived with the aim of providing high levels of automation to create an industrial-like environment for protein crystallography. A new software suite has been developed to permit reliable easy operation for the beamline users and beamline staff. High levels of diagnostics are built in to allow rapid trouble-shooting. These developments are now being exported to the ESRF macromolecular crystallography beamline complex and have been made in a modular fashion to facilitate transportability to other synchrotrons.

New approach to monitoring photon beam using visible light on VUV beamlines of compact storage ring HiSOR

A simple method to monitor the motion of photon beams using the visible component of synchrotron radiation (SR) is proposed, in which visible SR diagnostics are effectively extended. A preliminary test of the measurement principle was performed. We obtained a reasonable position response from photon beam fluctuation due to electron beam instability. With the aim of beam monitoring in user's beamlines of small storage rings, we discuss appropriate monitor assembly along with the advantages of the extension of visible diagnostics because the conventional photo–current method in VUV and X-ray regions is not applicable at the beamlines.

Status of the Novosibirsk terahertz FEL

The first stage of Novosibirsk high-power free-electron laser (FEL) was commissioned in 2003. It is based on the normal conducting CW energy recovery linac. Now the FEL provides electromagnetic radiation in the wavelength range 120–180 μm. The average power is 200 W. The minimum measured line width is 0.3%, which is close to the Fourier-transform limit. The assembly of user beamline is in progress. Plans of future developments are discussed.

Overview of insertion device controls at the Advanced Photon Source

The Advanced Photon Source (APS) is a third-generation synchrotron with major emphasis on insertion device (ID) sources. Currently, there are 25 sectors instrumented out of a possible 35 ID sources. Most of the insertion devices are undulators. Beamlines have been using the ID radiation at the APS for more than five years. The control system of choice at the APS is the experimental physics and industrial control system (EPICS) (http://www.aps.anl.gov/epics). Based on operational experience, the ID control system has been completely revamped. During user operations, the beamline user has complete control of the insertion device. Various interfaces, from RS-232 to EPICS channel access, have been provided for the users to control the IDs. The control system software has been designed to accommodate scanning of the insertion device synchronized to each user’s beamline monochromator. The users have the option of operating the device in a tapered mode. The control software allows the users to control the undulators in energy space from the fundamental to the seventh harmonic. The design philosophy of the insertion device control system will be discussed. The implementation and operational experience will be presented in detail.

VME insertion device control at the Advanced Photon Source

The Advanced Photon Source (APS) currently has 29 insertion devices (IDs) installed and operating. The need to remotely diagnose and correct problems has become increasingly important. This has been accomplished through the development of a new control system with greatly enhanced input/output (I/O) capabilities specifically targeted to this control task. The system features a custom VME control card and three rack-mounted interface chassis for ID control, encoder interface, and motor drive shutdown. The card provides device interlocks, limit switch logic, motor axis selection, digital I/O, and status feedback. This VME insertion device control was designed to operate with an eight-axis intelligent motor controller and a stepper-motor drive that accepts step and direction inputs. The front panel of the card has two connectors for all of the control signals for the stepper-motor drives. There is a third connector for the ID limit switch inputs and the emergency stop circuit, and a fourth connector provides 23 bits of digital outputs and 16 bits of digital inputs. Light-emitting diodes indicate which motions are inhibited by the limit switch logic. An experimental physics industrial control system (EPICS) (http://www.APS.ANL-GOV/EPICS) device driver was developed to access all the registers on the VME control card. Using standard EPICS records, the insertion device status can be viewed remotely. This minimizes downtime for APS ID beamline users by allowing faster resolution of any problems preventing a user from operating the insertion device. This new insertion device control has been in use at the APS since July of 1999. The design features of the control system and rationale for them will be presented, along with our experience in building, testing, installing, and operating the control system.

Secure network for beamline control

In SPring-8, beamline control system is constructed with a highly available distributed network system. The socket based communication protocol is used for the beamline control mainly. Beamline users can control the equipment by sending simple control commands to a server process, which is running on a beamline-managing computer (Ohata et al., SPring-8 beamline control system, ICALEPCS’99, Trieste, Italy, 1999). At the beginning the network was based on the shared topology at all beamlines. Consequently, it has a risk for misapplication of the user's program to access different machines on the network system cross over beamlines. It is serious problem for the SPring-8 beamline control system, because all beamlines controlled with unified software interfaces. We introduced the switching technology and the firewalls to support network access control. Also the virtual networking (VLAN: IEEE 802.1Q) and the gigabit Ethernet technology (IEEE 802.3ab) are introduced. Thus the network security and the reliability are guaranteed at the higher level in SPring-8 beamline.

Revolver undulator for BL15XU at SPring-8

We have developed and installed a revolver type undulator for a contract beamline (BL15XU) at SPring-8. Since wide energy range photons (0.5–60 keV) are used for the research in advanced materials at BL15XU, the revolver undulator has two pairs of undulator magnet arrays; one is a planar undulator for X-ray radiation and the other is a helical undulator for soft X-ray radiation. The two undulators are mounted on the same top and bottom rotatable magnet beams by 90°, and the beamline users can switch the undulators at anytime without any observable effect on the electron beam orbit and the photon beam position.

A high-throughput x-ray microtomography system at the Advanced Photon Source

A third-generation synchrotron radiation source provides enough brilliance to acquire complete tomographic data sets at 100 nm or better resolution in a few minutes. To take advantage of such high-brilliance sources at the Advanced Photon Source, we have constructed a pipelined data acquisition and reconstruction system that combines a fast detector system, high-speed data networks, and massively parallel computers to rapidly acquire the projection data and perform the reconstruction and rendering calculations. With the current setup, a data set can be obtained and reconstructed in tens of minutes. A specialized visualization computer makes rendered three-dimensional (3D) images available to the beamline users minutes after the data acquisition is completed. This system is capable of examining a large number of samples at sub-μm 3D resolution or studying the full 3D structure of a dynamically evolving sample on a 10 min temporal scale. In the near future, we expect to increase the spatial resolution to below 100 nm by using zone-plate x-ray focusing optics and to improve the time resolution by the use of a broadband x-ray monochromator and a faster detector system.

Status of the Advanced Photon Source at Argonne National Laboratory (invited)

The Advanced Photon Source at Argonne National Laboratory is a third-generation light source optimized for production of high-brilliance undulator radiation in the hard x-ray portion of the spectrum. A user community representing all major centers of synchrotron research, including universities, industry, and federal laboratories, will utilize these x-ray beams for investigations across a diverse range of disciplines. All technical facilities and components required for operations have been completed and installed, and are well along in the commissioning process. Major design goals and Department of Energy milestones have been met or exceeded. Project funds have been maximized to construct a number of beamline components and user facilities over and above those called for in the original project scope. Research teams preparing experimental apparatus at the Advanced Photon Source have procured strong funding support.

The Elettra beam line control system

Elettra is a third generation Synchrotron Light Source located in Trieste (Italy). It consists of a full energy linac injector and a storage ring with beam energies between 1.5 and 2 GeV. The facility is scheduled to be operational by end 1993. For the whole project 22 beam lines from insertion devices are foreseen, each of them is composed of a large number of measurement and controls instruments, most of them embedded in intelligent devices; in addition each beam line can be considered unique compared to the others, having been designed to provide a different kind of synchrotron radiation. This results in a large not homogenous environment where more than 200,000 physical points have to be controlled. A joint team composed of Softeco Sismat and Digital Equipment has developed a fully automated beam line control system able to give full remote controls, with different kind of access rights, to beam line users and beam line specialists as well as a full integration with experiment control systems.

National synchrotron light source beam line data acquisition and analysis computer system

A versatile computer environment to manage instrumentation alignment and experimental control at the National Synchrotron Light Source beam lines has been developed. The system is based on a 386 486 personal computer running under a UNIX operating system with X11 Windows. It offers an ideal combination of capability, flexibility, compatibility, and cost. With a single personal computer, the beam line user can run a wide range of scattering and spectroscopy experiments using a multi-tasking data-collection program which can interact with CAMAC, GPIB and AT-Bus interfaces, and simultaneously examine and analyze data and communicate with remote network nodes.