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auto3dem:documentation [2015/04/14 14:07] gcardone |
auto3dem:documentation [2019/06/19 16:22] (current) |
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| ==== Auto3DEM ==== | ==== Auto3DEM ==== | ||
| - | * User's guide ([[http://cryoem.ucsd.edu/programs/auto3dem_usersguide_v4.04.pdf|PDF]]) ([[http://cryoem.ucsd.edu/programs/auto3dem_usersguide_v4.04.htm|HTML]]) | + | * [[auto3dem:install|Installation]] |
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| + | * [[auto3dem:userguide|User Guide]] | ||
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| + | * [[auto3dem:extra_tools|Auxiliary programs]] | ||
| * Protocols | * Protocols | ||
| + | * [[auto3dem:documentation:protocols:initial_model|Generating a starting model]] | ||
| + | * [[auto3dem:documentation:protocols:focused_refinement|Mask-focused refinement]] | ||
| * [[auto3dem:documentation:protocols:asymmetric_reconstruction|Asymmetric reconstruction]] | * [[auto3dem:documentation:protocols:asymmetric_reconstruction|Asymmetric reconstruction]] | ||
| * [[auto3dem:documentation:protocols:gold_standard|Gold Standard procedure]] | * [[auto3dem:documentation:protocols:gold_standard|Gold Standard procedure]] | ||
| - | + | * Documentation for the parallel programs called by Auto3DEM (PDFs) [:!: last updated Oct 2004] | |
| - | * Documentation for parallel programs called by Auto3DEM (PDFs) | + | * [[http://bakerlab.ucsd.edu/programs/p3dr.pdf|P3DR]] 3D image reconstruction |
| - | * [[http://cryoem.ucsd.edu/programs/p3dr.pdf|P3DR]] 3D image reconstruction | + | * [[http://bakerlab.ucsd.edu/programs/pcut.pdf|PCUT]] Cutting spherical annulus from map |
| - | * [[http://cryoem.ucsd.edu/programs/pcut.pdf|PCUT]] Cutting spherical annulus from map | + | * [[http://bakerlab.ucsd.edu/programs/por.pdf|POR]] Local refinement of image origins and orientations |
| - | * [[http://cryoem.ucsd.edu/programs/por.pdf|POR]] Local refinement of image origins and orientations | + | * [[http://bakerlab.ucsd.edu/programs/pftsearch.pdf|PPFT]] Local refinement of image origins and orientations |
| - | * [[http://cryoem.ucsd.edu/programs/pftsearch.pdf|PPFT]] Local refinement of image origins and orientations | + | * [[http://bakerlab.ucsd.edu/programs/psf.pdf|PSF]] Structure factor determination and FSC calculation |
| - | * [[http://cryoem.ucsd.edu/programs/psf.pdf|PSF]] Structure factor determination and FSC calculation | + | \\ |
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| ==== RobEM === | ==== RobEM === | ||
| - | * User's Guide ([[http://cryoem.ucsd.edu/programs/robem_usersguide_v4.01.pdf|PDF]]) ([[http://cryoem.ucsd.edu/programs/robem_usersguide_v4.01.htm|HTML]]) | + | * User's Guide ([[http://bakerlab.ucsd.edu/programs/robem_usersguide_v4.01.pdf|PDF]]) ([[http://bakerlab.ucsd.edu/programs/robem_usersguide_v4.01.htm|HTML]]) |