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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]] |
- | Documentation for parallel programs called by Auto3DEM (PDFs) | + | * [[auto3dem:userguide|User Guide]] |
- | * [[http://cryoem.ucsd.edu/programs/p3dr.pdf|P3DR]] 3D image reconstruction | + | |
- | * [[http://cryoem.ucsd.edu/programs/pcut.pdf|PCUT]] Cutting spherical annulus from map | + | |
- | * [[http://cryoem.ucsd.edu/programs/por.pdf|POR]] Local refinement of image origins and orientations | + | |
- | * [[http://cryoem.ucsd.edu/programs/pftsearch.pdf|PPFT]] Local refinement of image origins and orientations | + | |
- | * [[http://cryoem.ucsd.edu/programs/psf.pdf|PSF]] Structure factor determination and FSC calculation | + | |
+ | * [[auto3dem:extra_tools|Auxiliary programs]] | ||
+ | |||
+ | * 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:gold_standard|Gold Standard procedure]] | ||
+ | |||
+ | * Documentation for the parallel programs called by Auto3DEM (PDFs) [:!: last updated Oct 2004] | ||
+ | * [[http://bakerlab.ucsd.edu/programs/p3dr.pdf|P3DR]] 3D image reconstruction | ||
+ | * [[http://bakerlab.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://bakerlab.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 | ||
+ | \\ | ||
+ | \\ | ||
==== 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]]) |