title: A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the contrast transfer function.
abstract: We describe a fast and accurate method for the reconstruction of macromolecular complexes from a set of projections. Direct Fourier inversion (in which the Fourier Slice Theorem plays a central role) is a solution for dealing with this inverse problem. Unfortunately, the set of projections provides a non-equidistantly sampled version of the macromolecule Fourier transform in the single particle field (and, therefore, a direct Fourier inversion) may not be an optimal solution. In this paper, we introduce a gridding-based direct Fourier method for the three-dimensional reconstruction approach that uses a weighting technique to compute a uniform sampled Fourier transform. Moreover, the contrast transfer function of the microscope, which is a limiting factor in pursuing a high resolution reconstruction, is corrected by the algorithm. Parallelization of this algorithm, both on threads and on multiple CPU's, makes the process of three-dimensional reconstruction even faster. The experimental results show that our proposed gridding-based direct Fourier reconstruction is slightly more accurate than similar existing methods and presents a lower computational complexity both in terms of time and memory, thereby allowing its use on larger volumes. The algorithm is fully implemented in the open-source Xmipp package and is downloadable from http://xmipp.cnb.csic.es.
authors.affiliation: Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/Darwin 3, Cantoblanco, 28049 Madrid, Spain.
authors.forename: V
authors.initials: V
authors.lastname: Abrishami
authors.affiliation: Unidad Asociada al CSIC, 'Supercomputación y Algoritmos', Universidad Almería & Málaga, Spain.
authors.forename: J R
authors.initials: JR
authors.lastname: Bilbao-Castro
authors.affiliation: Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/Darwin 3, Cantoblanco, 28049 Madrid, Spain.
authors.forename: J
authors.initials: J
authors.lastname: Vargas
authors.affiliation: Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/Darwin 3, Cantoblanco, 28049 Madrid, Spain; Escuela Politécnica Superior, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente, Cantoblanco, 28049 Madrid, Spain.
authors.forename: R
authors.initials: R
authors.lastname: Marabini
authors.affiliation: Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/Darwin 3, Cantoblanco, 28049 Madrid, Spain.
authors.forename: J M
authors.initials: JM
authors.lastname: Carazo
authors.affiliation: Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/Darwin 3, Cantoblanco, 28049 Madrid, Spain; Bioengineering Lab, Escuela Politecnica Superior, University San Pablo CEU, Boadilla del Monte, 28668 Madrid, Spain. Electronic address: coss@cnb.csic.es.
authors.forename: C O S
authors.initials: CO
authors.lastname: Sorzano
keywords: CTF correction; Cryo-electron microscopy; Single Particle Analysis; Three-dimensional reconstruction