Appion

h1. Appion Processing

## [[Terminology]]

## [[Common Workflow]]

## [[Processing Cluster Login]]

## [[Particle Selection]]

### [[Template Picking]]

### [[Dog Picking]]

### [[Signature]]

### [[Manual Picking]] 

### [[Repeat from other session]]

### [[Align and Edit Tilt Pairs]]

### [[Auto Align Tilt Pairs]]

## [[CTF Estimation]]

### [[Ace Estimation]]

### [[Ace 2 Estimation]]

### [[CtfTilt Estimation]]

### [[Repeat from other session]]

## [[Stacks]]

### [[Stack creation]]

### [[more stack tools]]

## [[Particle Alignment]]

### [[Run Alignment]]

### [[Run Feature Analysis]]

### [[Run Particle Clustering]]

## [[Ab Initio Reconstruction]]

### [[RCT Volume]]

### [[OTR Volume]]

### [[EMAN Common Lines]]

### [[IMAGIC Angular Reconstitution]]

## [[Refine Reconstruction]]

### [[EMAN Refinement]]

## [[Import Tools]]

### [[PDB tp Model]]

### [[EMDB to Model]]

### [[Upload Particles]]

### [[Upload Template]]

### [[Upload Model]]

### [[Upload More Images]]

### [[Upload Stack]]

## [[Image Assessment]]

### [[Web Img Assessment]]

### [[Multi Img Assessment]]

### [[Run Image Rejector]]

## [[Region Mask Creation]]

### [[Crud Finding]]

### [[Manual Masking]] 

## [[Synthetic Data]]

### [[Synthetic Dataset Creation]]

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

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