====== Documentation ======
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==== Auto3DEM ====

  * [[auto3dem:install|Installation]]

  * [[auto3dem:userguide|User Guide]]

  * [[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
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==== RobEM ===

  * 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]])