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auto3dem:documentation [2015/04/14 17:14]
gcardone
auto3dem:documentation [2015/12/22 18:06]
gcardone
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 ==== Auto3DEM ==== ==== Auto3DEM ====
  
-  * [[auto3dem:installation|Installation]] +  * [[auto3dem:install|Installation]] 
-  * 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:userguide|User Guide]] 
 + 
 +  * [[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://​cryoem.ucsd.edu/​programs/​p3dr.pdf|P3DR]] 3D image reconstruction     * [[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/​pcut.pdf|PCUT]] Cutting spherical annulus from map
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     * [[http://​cryoem.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://​cryoem.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
 +\\ 
 +\\
 ==== RobEM === ==== RobEM ===