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. 2010 Nov;17(6):774-81.
doi: 10.1107/S0909049510028566. Epub 2010 Sep 3.

Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice/DCS control system

Scott Classen  1 , Ivan Rodic, James Holton, Greg L Hura, Michal Hammel, John A Tainer
Affiliations

Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice/DCS control system

Scott Classen et al. J Synchrotron Radiat. 2010 Nov.

Abstract

Biological small-angle X-ray scattering (SAXS) provides powerful complementary data for macromolecular crystallography (MX) by defining shape, conformation and assembly in solution. Although SAXS is in principle the highest throughput technique for structural biology, data collection is limited in practice by current data collection software. Here the adaption of beamline control software, historically developed for MX beamlines, for the efficient operation and high-throughput data collection at synchrotron SAXS beamlines is reported. The Blu-Ice GUI and Distributed Control System (DCS) developed in the Macromolecular Crystallography Group at the Stanford Synchrotron Radiation Laboratory has been optimized, extended and enhanced to suit the specific needs of the biological SAXS endstation at the SIBYLS beamline at the Advanced Light Source. The customizations reported here provide a potential route for other SAXS beamlines in need of robust and efficient beamline control software. As a great deal of effort and optimization has gone into crystallographic software, the adaption and extension of crystallographic software may prove to be a general strategy to provide advanced SAXS software for the synchrotron community. In this way effort can be put into optimizing features for SAXS rather than reproducing those that have already been successfully implemented for the crystallographic community.

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Figures

Figure 1
Figure 1
Schematic diagram illustrating the organization of the DCS Server (DCSS), the Distributed Hardware Servers (DHSs) and the Blu-Ice GUI connections.
Figure 2
Figure 2
Collect tab of Blu-Ice for SAXS. Individual experimental run tabs (0, 1 and *) are located on the right side of the Collect tab. The snapshot tab (Tab 0) allows individual control of the sample-loading robot and the detector. Fully automated experimental runs are defined in run tabs 1–14. New tabs are generated by clicking on the * tab. A video widget allows the user to watch their sample as it is loaded into the cell, and an image-viewing window shows the most recent scattering data in the left side of the window.
Figure 3
Figure 3
Screening tab of Blu-Ice for SAXS. The spreadsheet defining the SAXS experiment is imported into the upper left panel, screening actions to be performed on each sample are defined in the upper right, scheduled tasks are dynamically updated in the lower right, and the video widget is located in the lower left panel.
Figure 4
Figure 4
Control demonstrating efficient removal of solution by liquid-handling robot. (a) Data collected from a 3 mg ml−1 xylanase solution with a matching buffer collected before and after the protein solution. No washing steps were performed between exposures. The blue curve has the first buffer subtracted and the black curve has the second buffer subtracted. (b) Raw data from the two buffers have been overlaid to show that there is no carry over of the xylanase when measuring the second buffer.
Figure 5
Figure 5
Schematic timeline depicting how the expose scripted operation coordinates the X-ray shutter, detector and the acquisition of critical X-ray intensity data.
Figure 6
Figure 6
Bubble detection. The top image is a bubble-free sample. The middle image shows an example of a bubble that is outside of the ROI and will not affect the SAXS experiment (formula image ≃ 400). The bottom image shows an example of a bubble that would be very problematic for collecting high-quality SAXS data (formula image ≃ 2000).
Figure 7
Figure 7
Bubble factor. This graph illustrates the stability of the bubble factor (formula image) over a 24 h period during which time 980 exposures were collected. During the collection there was one sample, beginning at exposure #533, that contained multiple bubbles in the ROI and a second sample, beginning at exposure #602, that was incompletely loaded with the meniscus located within the ROI.
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