AutoPX: a new software package to process X-ray diffraction data from biomacromolecular crystals

Abstract

A new software package, autoPX, for processing X-ray diffraction data from biomacromolecular crystals is reported. This processing software package is designed on the basis of novel methods such as the location of diffraction spots by an improved Canny operator, indexing by a modified Fourier transform, a novel definition of mosaicity that expresses the dispersion state of reciprocal diffraction spots, and the correction of predicted diffraction spot coordinates by homography transform. New programming of some traditional algorithms necessary for integration and scaling is also included. Several examples of crystal structure determination using data from the SSRF beamlines reduced using autoPX, HKL-2000, DIALS and XDS are also demonstrated, and indicate that autoPX is capable of processing diffraction data from biomacromolecular crystals and providing adequate solutions to problems encountered at the SSRF beamlines.

Structural basis of the farnesoid X receptor/retinoid X receptor heterodimer on inverted repeat DNA

“…The best data were collected in the Beamline BL17U1 of Shanghai Synchrotron Radiation Facility (SSRF) and reduced by AutoPX [48] . The structure of the FXR-DBD/RXR-DBD/IR1 complex was solved by molecular replacement (MR) using phaser from the PHENIX package using the ecdysone receptor (EcR)/ultraspiracle (USP)/IR1 (PDB ID: 1R0N) as a search model [49] .…”

Upgrade of crystallography beamline BL19U1 at the Shanghai Synchrotron Radiation Facility

“…For users who may prefer or need to process diffraction data manually, our system also accommodates their preferences. We offer the HKL3000 (Minor et al, 2006) and AUTOPX (Wang et al, 2022) software tools, providing users with convenient and swift options for manually processing data. This dual approach caters to the diverse needs of researchers, ensuring a seamless and efficient experience in handling diffraction data.…”

An Intelligent Data Analysis System for Biological Macromolecule Crystallography

“…AutoPX [12] and autoPROC [13] are automated pipelines that integrate multiple software tools for data processing and analysis, providing streamlined workflows for crystallographers. Phaser [14] is a widely used program for molecular replacement, a technique used to determine the phase information of a crystal structure.…”