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Appion Processing » History » Revision 49

Revision 48 (Dmitry Lyumkis, 08/02/2011 12:32 PM) → Revision 49/69 (Dmitry Lyumkis, 07/16/2012 05:38 PM)

h1. Appion Processing 

 ## *[[Terminology]]* 
 ## *[[Common Workflow]]* 
 *** [[Step by Step Guide]] 
 *** [[Quality Assessment]] 
 *** [[Random-Conical Tilt (RCT) Reconstruction workflow]] 
 ## *[[Processing Cluster Login]]* 
 ## *[[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]]*  
 *** [[Ace Estimation]] 
 *** [[Ace 2 Estimation]] 
 *** [[CtfFind Estimation]] 
 *** [[Repeat from other session]] 
 ## *[[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]]*  
 ### [[Run Alignment]] 
 **** [[Xmipp Maximum Likelihood Alignment]] 
 **** [[Spider Reference-free Alignment]] 
 **** [[IMAGIC Multi Reference 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]] 
 **** [[IMAGIC Multivariate Statistical Analysis (MSA)]] 
 **** [[Xmipp Rotational Kerden Self-Organizing Map]] 
 **** [[Cluster by Affinity Propogation]] 
 ### [[Run Particle Clustering]] 
 ## *[[Ab Initio Reconstruction]]* 
 *** [[RCT Volume]]  
 *** [[OTR Volume]]  
 *** [[EMAN Common Lines]]  
 *** [[IMAGIC Angular Reconstitution]]  
 ## *[[Refine Reconstruction]]*  
 *** [[EMAN Refinement]] 
 *** [[Frealign Refinement]] 
 *** [[SPIDER Refinement]] 
 *** [[IMAGIC Refinement]] 
 *** [[Refinement Post-processing Procedures]] 
 ## *[[Helical Processing]]*  
 *** [[Helical Image Processing (PHOELIX)]] 
 ## *[[Tomography]]* 
 ### [[Align tilt series]] 
 ### [[Create full tomogram]] 
 ### [[Upload_full_tomogram|Upload tomogram]] 
 ### [[Create tomogram subvolume]] 
 ### [[Average tomogram subvolumes]] 
 ## *[[Import Tools]]*  
 *** [[PDB to Model]] 
 *** [[EMDB to Model]] 
 *** [[Upload Particles]] 
 *** [[Upload Template]] 
 *** [[Upload Model]] 
 *** [[Upload More Images]] 
 *** [[Upload Stack]] 
 *** [[Upload Refinement]] 
 ## *[[Image Assessment]]*  
 *** [[Web Img Assessment]] 
 *** [[Multi Img Assessment]] 
 *** [[Run Image Rejector]] 
 ## *[[Region Mask Creation]]* 
 *** [[Manual Masking]]  
 ## *[[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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