https://bakerlab.ucsd.edu/wikis/software/ 2026-05-10T06:55:21-07:00 https://bakerlab.ucsd.edu/wikis/software/ https://bakerlab.ucsd.edu/wikis/software/lib/tpl/bootstrap3/images/favicon.ico text/html 2015-04-15T10:51:34-07:00 https://bakerlab.ucsd.edu/wikis/software/start.php?id=auto3dem:documentation:protocols:asymmetric_reconstruction&rev=1429120294&do=diff Reconstruction of asymmetric components in icosahedral structures A practical approach is to first process the data by ignoring the presence of any asymmetric component, thus just exploiting the symmetric properties of the structure. Since a symmetrized reconstruction will be used at each iteration, determination of the orientation and centre for each particle is expected to be sufficiently accurate, under the assumption that the additional component only minimally affects such determination. O… text/html 2015-12-22T17:49:21-07:00 https://bakerlab.ucsd.edu/wikis/software/start.php?id=auto3dem:documentation:protocols:focused_refinement&rev=1450835361&do=diff Mask-focused refinement Starting with the version 4.05.2 of Auto3DEM, it is possible to refine the orientation and the origin of the particles while focusing on a sub-volume of interest. This is advantageous, for example, when trying to determine the structure of an asymmetric feature in a icosahedral model. The approach implemented is to define a sub-volume by means of a binary mask, so that the reference map will only contain the region of interest. The volume excluded can then be interpreted… text/html 2015-07-08T11:09:53-07:00 https://bakerlab.ucsd.edu/wikis/software/start.php?id=auto3dem:documentation:protocols:gold_standard&rev=1436378993&do=diff Gold Standard reconstruction Starting with the version 4.05 of Auto3DEM, it is possible to follow what has been recently defined as the 'gold standard procedure' (called 'unbiased model reconstruction method' in the original paper on Auto3DEM by Yan et. al, 2007), in a way that is almost transparent to the user. The procedure consists of splitting the data into two half sets of particles, at the beginning of the iterative alignment: at each iteration each set generates an independent reconstruc… text/html 2019-06-19T16:22:17-07:00 https://bakerlab.ucsd.edu/wikis/software/start.php?id=auto3dem:documentation:protocols:initial_model&rev=1560986537&do=diff Generating a starting model Obtaining a reconstructed density map from a set of particles is an iterative process that requires an initial reference volume, typically a low-resolution reconstruction from the same or a similar sample. When a starting model is not available, one can easily be constructed for icosahedral viruses using the program