https://bakerlab.ucsd.edu/wikis/software/ 2026-05-03T12:32:16-07:00 https://bakerlab.ucsd.edu/wikis/software/ https://bakerlab.ucsd.edu/wikis/software/lib/tpl/bootstrap3/images/favicon.ico text/html 2019-06-19T16:22:17-07:00 https://bakerlab.ucsd.edu/wikis/software/start.php?id=auto3dem:documentation&rev=1560986537&do=diff Documentation Auto3DEM * Installation * User Guide * Auxiliary programs * Protocols * Generating a starting model * Mask-focused refinement * Asymmetric reconstruction * Gold Standard procedure * Documentation for the parallel programs called by Auto3DEM (PDFs) [:!: last updated Oct 2004] * P3DR 3D image reconstruction * PCUT Cutting spherical annulus from map text/html 2019-06-19T16:22:17-07:00 https://bakerlab.ucsd.edu/wikis/software/start.php?id=auto3dem:download&rev=1560986537&do=diff Download The software is provided only as source code. Installation instructions Software change history Current version: AUTO3DEM ver. 4.05.2 December 22, 2015 Older versions: AUTO3DEM ver. 4.05.1 July 8, 2015 AUTO3DEM v 4.05 December 23, 2014 AUTO3DEM v 4.04.1 March 21, 2014 AUTO3DEM v 4.04 March 11, 2014 AUTO3DEM v 4.03.1 July 22, 2013 AUTO3DEM v 4.03 May 1, 2013 AUTO3DEM v 4.02 June 19, 2012 AUTO3DEM v 4.01.12 December 6, 2011 text/html 2019-06-19T16:22:17-07:00 https://bakerlab.ucsd.edu/wikis/software/start.php?id=auto3dem:extra_tools&rev=1560986537&do=diff Auxiliary Programs In addition to the main program auto3dem, the package provides additional programs to perform additional processing or analysis. a3dm tools These are programs all starting with the prefix a3dm_, which mostly support the user during the analysis of the results from running auto3dem. They are all written in python language, and some of them require modules (e.g. numpy, matplotlib, tkinter) that are available on most Linux text/html 2015-12-22T12:59:58-07:00 https://bakerlab.ucsd.edu/wikis/software/start.php?id=auto3dem:history&rev=1450817998&do=diff Modification history This document describes incremental modifications made to the Baker lab software suite. Since the image preprocessing, image reconstruction, format conversion, and utility programs are so tightly coupled (e.g. shared standards and libraries) and released as a single package, all modifications are described together in a single document. Owing to the complexity of the software, it is impractical to provide a line-by-line listing of alterations. Instead we focus primarily on … text/html 2019-06-19T16:22:17-07:00 https://bakerlab.ucsd.edu/wikis/software/start.php?id=auto3dem:home&rev=1560986537&do=diff Auto3DEM Auto3DEM is a semi-automated image reconstruction system that provides all the tools to process raw micrographs acquired at an electron microscope and generate a three-dimensional reconstruction. The most intensive computational procedure like orientation search and reconstruction can be executed either in serial or in parallel on a computer cluster. A graphical interface, RobEM, is also provided both for image processing and visualization purposes. text/html 2015-07-07T19:06:28-07:00 https://bakerlab.ucsd.edu/wikis/software/start.php?id=auto3dem:install&rev=1436321188&do=diff Installation Quick start * Download the latest version from the website * Uncompress the archive downloaded * Move the directory to the directory where you want to install the programs * Open a terminal and launch the installation script text/html 2015-07-07T16:54:43-07:00 https://bakerlab.ucsd.edu/wikis/software/start.php?id=auto3dem:license&rev=1436313283&do=diff Copyright© 2015 Baker Lab, University of California San Diego. All Rights Reserved. END-USER LICENSE AGREEMENT PLEASE READ THIS DOCUMENT CAREFULLY. By installing or using this software you agree with the terms and conditions of this license agreement. If you do not accept the terms of this license agreement you may not install or use this software. Permission to copy, modify, and distribute this software and its documentation for educational, research and non-profit purposes, without fee, and w… text/html 2016-01-19T13:04:35-07:00 https://bakerlab.ucsd.edu/wikis/software/start.php?id=auto3dem:userguide&rev=1453237475&do=diff Auto3DEM User Guide Introduction Auto3DEM is an automated system for 3D structure determination from images of vitrified particles. The software was specifically developed for icosahedral viruses, but should be able to handle particles of any symmetry as long as the particles are roughly spherical and their images can readily be divided into circular annuli. Even this restriction can be relaxed if auto3dem is run in refine mode from the beginning: if initial orientations for the images are not…