Strul--a method for 3D alignment of single-particle projections based on common line correlation in Fourier space

A central problem of 3D reconstruction in single-particle electron microscopy is the determination of relative orientations of the individual projections contributing to the reconstruction. This article describes an implementation of the method of common lines correlation in Fourier space that allows generation of common lines between an arbitrary number of projections which might posses an arbitrary point group symmetry. Based on this method, it is possible to optimize rotational and translational alignment parameters for individual single-particle projections. The underlying philosophy and details of implementation are discussed, and as an illustration a 3D reconstruction in ice of peroxisomal alcohol oxidase from Pichia pastoris, an octameric assembly with 422-symmetry and a molecular weight of 592 kDa is presented.