The slip-and-slide algorithm: a refinement protocol for detector geometry

Ginn, H.; Stuart, David I.

doi:10.1107/s1600577517013327

Cited by 5 publications

(4 citation statements)

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“…Indexing was done for both data sets applying CrystFEL v.0.6.3 to peaks found by Cheetah using the indexing packages MOSFLM 42 , DirAx 43 and asdf 26 . Since detector panel locations were not measured to adequate precision before the experiment, lithium titanate powder diffraction rings were used for rough detector panel alignment followed by fine refinement from HEWL and CTX-M-14 diffraction data using geoptimiser 44 and Slip-n-slide 45 . Combined with a 1% uncertainty in photon energy and uncertainty in the detector-to-sample distance, final indexing involved an iterative process with refinement of all unknown values using geoptimiser 44 .…”

Section: Methodsmentioning

confidence: 99%

Megahertz serial crystallography

et al. 2018

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The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.

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Section: Methodsmentioning

confidence: 99%

Megahertz serial crystallography

et al. 2018

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“…Unfortunately, like hit finding and detector-readout intensity calibration, creating and refining a geometry file for a complicated multipanel detector is a daunting task, and is itself the subject of entire papers (Yefanov et al, 2015;Ginn & Stuart, 2017;Brewster et al, 2014). Some example geometry files are distributed with CrystFEL, which can be used as templates, including examples for the CSPAD detector at LCLS in two different datafile layouts (see Fig.…”

Section: Figurementioning

confidence: 99%

Processing serial crystallography data with CrystFEL: a step-by-step guide

White

2019

Acta Crystallogr D Struct Biol

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“…xfel (Hattne et al, 2014), geoptimiser (Yefanov et al, 2015) in CrystFEL, DIALS (Waterman et al, 2016;Brewster et al, 2018) and cppxfel (Ginn & Stuart, 2017). In ClickX, we focus on refining parameters associated with single-panel detectors (or multi-panel detectors with well determined metrology) using powder diffraction signals, including the photon energy (), detector distance (D), beam center (c x ; c y ) and detector tilting angles ( t ; t ).…”

Section: Geometry Calibrationmentioning

confidence: 99%

ClickX: a visualization-based program for preprocessing of serial crystallography data

Liu

2019

J Appl Cryst

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Serial crystallography is a powerful technique in structure determination using many small crystals at X-ray free-electron laser or synchrotron radiation facilities. The large diffraction data volumes require high-throughput software to preprocess the raw images for subsequent analysis. ClickX is a program designated for serial crystallography data preprocessing, capable of rapid data sorting for online feedback and peak-finding refinement by parameter optimization. The graphical user interface (GUI) provides convenient access to various operations such as pattern visualization, statistics plotting and parameter tuning. A batch job module is implemented to facilitate large-data-volume processing. A two-step geometry calibration for single-panel detectors is also integrated into the GUI, where the beam center and detector tilting angles are optimized using an ellipse center shifting method first, then all six parameters, including the photon energy and detector distance, are refined together using a residual minimization method. Implemented in Python, ClickX has good portability and extensibility, so that it can be installed, configured and used on any computing platform that provides a Python interface or common data file format. ClickX has been tested in online analysis at the Pohang Accelerator Laboratory X-ray Free-Electron Laser, Korea, and the Linac Coherent Light Source, USA. It has also been applied in post-experimental data analysis. The source code is available via https://github.com/LiuLab-CSRC/ClickX under a GNU General Public License.

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The slip-and-slide algorithm: a refinement protocol for detector geometry

Cited by 5 publications

References 20 publications

Megahertz serial crystallography

Megahertz serial crystallography

Processing serial crystallography data with CrystFEL: a step-by-step guide

ClickX: a visualization-based program for preprocessing of serial crystallography data

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