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Code outputs and figures from "Efficient high-resolution refinement in cryo-EM with stochastic gradient descent"

Name: Code outputs and figures from "Efficient high-resolution refinement in cryo-EM with stochastic gradient descent"
Creator: Toader, Bogdan

Research datakeyboard_double_arrow_right Dataset 31 Oct 2024Embargo end date: 24 Jun 2025Publisher:Zenodo

Authors: Toader, Bogdan;

doi: 10.5281/zenodo.15728764 , 10.5281/zenodo.14017756 , 10.5281/zenodo.14017757

Code outputs and figures from "Efficient high-resolution refinement in cryo-EM with stochastic gradient descent"

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Abstract

Code outputs and figures for the numerical experiments on preconditioned SGD for cryo-EM reconstruction for reproducing the results in the article: Efficient high-resolution refinement in cryo-EM with stochastic gradient descent. Bogdan Toader, Marcus A. Brubaker, Roy R. Lederman Acta Crystallographica Section D, 2025 The outputs are obtained by running the Jupyter notebooks in the notebooks/preconditioned_sgd directory in the GitHub repository (release v0.2): https://github.com/bogdantoader/simplecryoem The particle images used for these experiments can be downloaded from EMPIAR-10076 and require inverting the contrast. The file containing the pose variables and CTF parameters is the particles_file/my_particles_8.star file in the attached archive.

Related Organizations

Medical Research Council
United Kingdom
MRC Laboratory of Molecular Biology
United Kingdom

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