Abstract
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.
Highlights
Great success has been achieved in macromolecular structure determination by serial femtosecond crystallography (SFX) (Chapman et al, 2011; Boutet et al, 2012; Barends et al, 2014)
Using extremely bright X-ray freeelectron laser (XFEL) pulses, a diffraction signal can be detected to atomic resolution with micrometre-sized crystals at room temperature under a ‘diffract-before-destroy’ scheme (Neutze et al, 2000)
The femtosecond duration of XFEL pulses provides the unique advantage of probing fast dynamics in pump–probe experiments, useful in understanding light-triggered processes (Kupitz et al, 2014; Tenboer et al, 2014; Pande et al, 2016; Nogly et al, 2018)
Summary
Great success has been achieved in macromolecular structure determination by serial femtosecond crystallography (SFX) (Chapman et al, 2011; Boutet et al, 2012; Barends et al, 2014). In typical SX (including SFX) experiments, millions of raw images are collected to yield a complete data set that can be used for high-resolution structure determination (Liu & Spence, 2016). These data are often collected at high repetition rates, generating high throughput of raw data for the downstream analysis. Python-based cctbx.xfel (Sauter et al, 2013) provides an alternative data analysis pipeline, including preprocessing (e.g. geometry optimization and spot finding) and post-processing (e.g. indexing and merging). ClickX supports multiple data formats, and users can visualize a broad range of data types, including pixel values, individual diffraction patterns and statistical data from analyses
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