Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules

Peck, Ariana; Chang, Hsing-Yin; Dujardin, Antoine; Ramalingam, Deeban; Uervirojnangkoorn, Monarin; Wang, Zhaoyou; Mancuso, Adrian; Poitevin, Frédéric; Yoon, Chun Hong

doi:10.1107/s1600576722005994

Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules

Journal Article · Fri Jul 15 00:00:00 EDT 2022 · Journal of Applied Crystallography (Online)

DOI:https://doi.org/10.1107/s1600576722005994· OSTI ID:1886987

Peck, Ariana ^[1]; Chang, Hsing-Yin ^[2]; ^[2]; Ramalingam, Deeban ^[2]; Uervirojnangkoorn, Monarin ^[2]; ^[2]; ^[3]; Poitevin, Frédéric ^[2]; Yoon, Chun Hong ^[2]

SLAC National Accelerator Lab., Menlo Park, CA (United States). Linac Coherent Light Source (LCLS); SLAC
SLAC National Accelerator Lab., Menlo Park, CA (United States). Linac Coherent Light Source (LCLS)
European XFEL, Schenefeld (Germany); La Trobe Univ., Melbourne, VIC (Australia)

X-ray free-electron lasers (XFELs) have the ability to produce ultra-bright femtosecond X-ray pulses for coherent diffraction imaging of biomolecules. While the development of methods and algorithms for macromolecular crystallography is now mature, XFEL experiments involving aerosolized or solvated biomolecular samples offer new challenges in terms of both experimental design and data processing. Skopi is a simulation package that can generate single-hit diffraction images for reconstruction algorithms, multi-hit diffraction images of aggregated particles for training machine learning classifiers using labeled data, diffraction images of randomly distributed particles for fluctuation X-ray scattering algorithms, and diffraction images of reference and target particles for holographic reconstruction algorithms. Skopi is a resource to aid feasibility studies and advance the development of algorithms for noncrystalline experiments at XFEL facilities.

View Accepted Manuscript (DOE)

Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-76SF00515

OSTI ID:: 1886987

Journal Information:: Journal of Applied Crystallography (Online), Journal Name: Journal of Applied Crystallography (Online) Journal Issue: 4 Vol. 55; ISSN 1600-5767

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
fluctuation X-ray scattering
free-electron lasers
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simulation
single-particle imaging

Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules

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