Integrated software for macromolecular crystallography synchrotron beamlines II: revision, robots and a database

Abstract

This manuscript chronicles the evolution of software used originally to control a diffractometer at a macromolecular crystallography beamline. The system has been augmented and rewritten. A modular and carefully organized suite of programs now handles the whole experimental environment from a single vantage point. It provides automatic logging of the experiment and communication with the user, all the way from an initial proposal to perform the work to the end of data collection. This has included construction of a relational database to organize all details of the experiment and incorporation of a robotic specimen changer to provide automation for high-throughput applications.

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“…With 72 different optical spectra taken every 5° by rotating the crystal 360°, the optimal spectroscopic angle for the cryoloop and crystal was defined using CBASS software. 51 X-ray diffraction collection started with 180 × 1 °C rotation to acquire a full data set. During the readout of X-ray diffraction images, correlated electronic absorption spectra were collected with the crystal rotating to the optimal angle.…”

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“…Whilst collecting data at the synchrotron beamline, the user must make decisions about the parameters of the experiment—exposure time, rotation range, oscillation angle, detector distance, beam size and wavelength—based on their experience, visual inspection of the diffraction images and information output by data-processing packages. Most of the instrumentation in the experimental station is computationally controlled using software packages such as Blu - Ice (McPhillips et al 2002), CBASS (Skinner et al 2006), MxCube (Gabadinho et al 2010) and JBlue - Ice (Stepanov et al 2011). However, very often an intuitive decision is made by the user on the exposure time to use.…”

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“…As a result, the time involved to set up the experiment (sample mounting, crystal centering, and determination of data-collection parameters) has become a significant proportion of the total time. There are a number of beamlines partially dedicated to structural genomics projects including beamline X29 at National Synchrotron Light Source, aimed at automating routine processes as much as possible [68][69][70][71].…”

“…These systems also enable users to routinely and systematically screen hundreds of samples, considerably reducing the need for manual intervention. A number of groups have initiated projects to develop methods for automatic sample handling, with the ultimate goal being to fully automate the X-ray diffraction experiment [71][72][73][74][75][76][77][78][79]. Presently, there are three commercially available crystal mounting robots: a Cryogenic Sample Changer from Mar-Research, an Automated Crystal Transport Orientation and Retrieval technology from Rikagu, and Bruker-Nonius from Bruker AXS.…”