A common lines approach for \textit{ab initio} modeling of cyclically symmetric molecules

DOI10.1088/1361-6420/AB2FB2MaRDI QIDQ5204633zbMATH OpenOpenAlexFDO

Authors Gabi Pragier, Yoel Shkolnisky

Publication date 5 December 2019

Published in Inverse Problems (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1901.10888

zbMATH Keywords

synchronizationcryo-electron microscopysymmetric moleculesangular-reconstitution

Mathematics Subject Classification ID

Numerical methods for integral transforms (65R10) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10) General integral transforms (44A05)

Abstract: One of the challenges in single particle reconstruction in cryo-electron microscopy is to find a three-dimensional model of a molecule using its two-dimensional noisy projection-images. In this paper, we propose a robust "angular reconstitution" algorithm for molecules with $n$-fold cyclic symmetry, that estimates the orientation parameters of the projections-images. Our suggested method utilizes self common lines which induce identical lines within the Fourier transform of each projection-image. We show that the location of self common lines admits quite a few favorable geometrical constraints, thus allowing to detect them even in a noisy setting. In addition, for molecules with higher order rotational symmetry, our proposed method exploits the fact that there exist numerous common lines between any two Fourier transformed projection-images of such molecules, thus allowing to determine their relative orientation even under high levels of noise. The efficacy of our proposed method is demonstrated using numerical experiments conducted on simulated and experimental data.

Recommendations

• Common lines ab initio reconstruction of \(D_2\)-symmetric molecules in cryo-electron microscopy
• Orientation determination of cryo-EM images using least unsquared deviations
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Cites work

• Fundamentals of Computerized Tomography
• Integral geometry and three-dimensional reconstruction of randomly oriented identical particles from their electron microphotos
• Mathematical methods in image reconstruction
• The mathematics of computerized tomography
• Viewing angle classification of cryo-electron microscopy images using eigenvectors
• Viewing direction estimation in cryo-EM using synchronization

Cited in

(7)

• Common lines ab initio reconstruction of \(D_2\)-symmetric molecules in cryo-electron microscopy
• Method of moments for 3D single particle \textit{ab initio} modeling with non-uniform distribution of viewing angles
• Motion detection in diffraction tomography by common circle methods
• A Common Lines Approach for Ab Initio Modeling of Molecules with Tetrahedral and Octahedral Symmetry
• Semi-algebraic geometry of common lines
• Orientation determination of cryo-EM images using least unsquared deviations
• Averaging orientations with molecular symmetry in cryo-EM

Describes a project that uses

Uses Software

• Chimera
• EMPIAR
• ASPIRE

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