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auto3dem:documentation [2015/03/29 18:48]
gcardone created
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]]
  
-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]])