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Appion Processing » History » Revision 40

Revision 39 (Anke Mulder, 06/14/2010 03:09 PM) → Revision 40/69 (Amber Herold, 07/29/2010 02:00 PM)

h1. Appion Processing 

 ## *[[Terminology]]* [[Terminology]] 
 ## *[[Common Workflow]]* [[Common Workflow]] 
 *** [[Step by Step Guide]] 
 *** [[Quality Assessment]] 
 ## *[[Processing [[Processing Cluster Login]]* Login]] 
 ## *[[Particle [[Particle Selection]] * 
  
 *** [[Template Picking]] 
 *** [[Dog Picking]] 
 *** [[Manual Picking]]  
 *** [[Repeat from other session]] 
 *** [[Random Conical Tilt Picking]] 
 **** [[Align and Edit Tilt Pairs]] 
 **** [[Auto Align Tilt Pairs]] 
 ## *[[CTF Estimation]]* [[CTF Estimation]]  
 *** [[Ace Estimation]] 
 *** [[Ace 2 Estimation]] 
 *** [[CtfFind Estimation]] 
 *** [[Repeat from other session]] 
 ## *[[Stacks]]* [[Stacks]]  
 *** [[Stack creation]] 
 *** [[more stack tools]] 
 **** [[Combine Stacks]] 
 **** [[View Stacks]]  
 ***** [[Filter by MeanSTDev]] 
 ***** [[Center Particles]] 
 ***** [[Sort Junk]] 
 ***** [[Create Substack]] 
 **** [[Alignment SubStacks]] 
 **** [[ Jumpers SubStack]] 
 **** [[Convert Stack into Particle Picks]] 
 ## *[[Particle Alignment]]* [[Particle Alignment]]  
 ### [[Run Alignment]] 
 **** [[Xmipp Maximum Likelihood Alignment]] 
 **** [[Spider Reference-free Alignment]] 
 **** [[Spider Reference-based Alignment]] 
 **** [[Ed's Iteration Alignment]] 
 **** [[Xmipp Reference-based Maximum Likelihood Alignment]] 
 ### [[Run Feature Analysis]] 
 **** [[Spider Coran Classification]] 
 **** [[Xmipp Kerden Self-Organizing Map]] 
 **** [[Xmipp Rotational Kerden Self-Organizing Map]] 
 ### [[Run Particle Clustering]] 
 ## *[[Ab [[Ab Initio Reconstruction]]* Reconstruction]] 
 *** [[RCT Volume]]  
 *** [[OTR Volume]]  
 *** [[EMAN Common Lines]]  
 *** [[IMAGIC Angular Reconstitution]]  
 ## *[[Refine Reconstruction]]* [[Refine Reconstruction]]  
 *** [[EMAN Refinement]] 
 *** [[Frealign Refinement]] 
 *** [[SPIDER Refinement]] 
 *** [[IMAGIC Refinement]] 
 ## *[[Tomography]]* [[Tomography]] 
 ### [[Align tilt series]] 
 ### [[Create full tomogram]] 
 ### [[Upload_full_tomogram|Upload tomogram]] 
 ### [[Create tomogram subvolume]] 
 ### [[Average subvolumes]] 
 ## *[[Import Tools]]* [[Import Tools]]  
 *** [[PDB to Model]] 
 *** [[EMDB to Model]] 
 *** [[Upload Particles]] 
 *** [[Upload Template]] 
 *** [[Upload Model]] 
 *** [[Upload More Images]] 
 *** [[Upload Stack]] 
 ## *[[Image Assessment]]* [[Image Assessment]]  
 *** [[Web Img Assessment]] 
 *** [[Multi Img Assessment]] 
 *** [[Run Image Rejector]] 
 ## *[[Region [[Region Mask Creation]]* Creation]] 
 *** [[Manual Masking]]  
 ## *[[Synthetic Data]]* [[Synthetic Data]]  
 *** [[Synthetic Dataset Creation]] 


 !http://emg.nysbc.org/attachments/282/Picture_83.png! 
 !http://emg.nysbc.org/attachments/277/Picture_81.png! 





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 [[Appion and Leginon Database Tools|< Appion and Leginon Database Tools]] 

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