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AUTO3DEM (including RobEM) v 3.13. May 15, 2009

AUTO3DEM is an automated image reconstruction system that coordinates the execution of the parallel, numerically-intensive codes P3DR, PCUT, POR, PPFT, and PSF. The archives for v3.0 and later also include the complete source code for building RobEM, a GUI driven program used both for image preprocessing (particle boxing, blemish removal, apodization, normalization, gradient correction) and visualization.

To reference this program, please cite: Yan X., R.S. Sinkovits, and T.S. Baker (2007) AUTO3DEM - an automated and high throughput program for image reconstruction of icosahedral particles. J. Struct. Bio. 157:73-82. (PDF)

AUTO3DEM is free software, licensed under the BSD License .

AUTO3DEM, © 2006-2008, Regents of the University of California

Documentation (PDFs)
P3DR Parallel 3D image reconstruction program: October 29, 2004
PCUT Parallel code for cutting spherical annulus from map: November 10, 2004
POR Parallel code for determining particle image origins and orientations in refine mode
PPFT Parallel code for determining particle image origins and orientations in search mode (PFTSearch.pdf)
PSF Parallel structure factor determination code
AUTO3DEM Keywords: Description of keywords for automated image reconstruction system: May 15, 2009

AUTO3DEM Test Problem Documentation: This document describes how to run the test problem that is distributed with AUTO3DEM. The data set is derived from nine micrographs of frozen-hydrated reovirus. The necessary files are below. AUTO3DEM Modification History: May 15, 2009

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Produced by the Timothy S. Baker Cryoelectron Microscopy Laboratory
Main Address: Department of Chemistry and Biochemistry MC-0378,
University of California, San Diego,
9500 Gilman Dr., La Jolla, CA 92093-0378
© 2006-2009 Timothy S. Baker. Material may not be used or reproduced in any way without permission.
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Date Modified: May 15, 2009