https://bakerlab.ucsd.edu/wikis/software/ 2026-04-28T03:07:40-07:00 https://bakerlab.ucsd.edu/wikis/software/ https://bakerlab.ucsd.edu/wikis/software/lib/tpl/bootstrap3/images/favicon.ico text/html 2016-03-06T12:01:20-07:00 admin https://bakerlab.ucsd.edu/wikis/software/start.php?id=sidebar&rev=1457294480&do=diff * Auto3DEM * Download * Documentation * AutoRTM * LocalFSC * IHRSR++ * Internal text/html 2016-01-19T13:04:35-07:00 admin 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… text/html 2016-01-02T17:45:22-07:00 gcardone https://bakerlab.ucsd.edu/wikis/software/start.php?id=labprograms:alifraba&rev=1451785522&do=diff alifraba alifraba (align frames in background) is a program to align frames acquired from a K2 camera by means of Leginon. The program relies on IMOD routines for the alignment of the frames (tiltxcorr, newstack and avgstack). How it works The program uses an iterative approach to determine the shift to apply to each frame against an average reference, which is refined at each iteration (see documentation on text/html 2015-12-30T21:37:57-07:00 gcardone https://bakerlab.ucsd.edu/wikis/software/start.php?id=labprograms:rawtransferd&rev=1451540277&do=diff rawtransferd Rawtransferd is a daemon server running in background on the server borg. It is responsible for monitoring the directory on the K2 computer where the frames are saved by default by Leginon, and to transfer them to borg. Each time a new stack of frames is found, the program interrogates the Leginon database, and if the stack is linked to a session, then the file is renamed according to that session and transferred. text/html 2015-12-22T19:18:58-07:00 gcardone https://bakerlab.ucsd.edu/wikis/software/start.php?id=auto3dem:extra_tools&rev=1450840738&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 2015-12-22T18:06:45-07:00 gcardone https://bakerlab.ucsd.edu/wikis/software/start.php?id=auto3dem:documentation&rev=1450836405&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 2015-12-22T17:49:21-07:00 gcardone 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…