Appion

h1. Appion User Guide

# [[User Management]]

# [[Appion and Leginon Database Tools]]

## [[Image Viewer]]

## [[2 Way Viewer]]

## [[3 Way Viewer]]

## [[LOI]]

## [[RCT]]

## [[Tomography]]

## [[Dual Viewer]]

## [[Hole Template Viewer]]

## [[Administration]]

## [[Project DB]]

# [[Appion Processing]]

## [[Terminology]]

## [[Common Workflow]]

## [[Processing Cluster Login]]

## [[Particle Selection]]

### [[Template Picking]]

### [[Dog Picking]]

### [[Manual Picking]] 

## [[CTF Estimation]]

### [[Ace Estimation]]

### [[Ace 2 Estimation]]

### [[CtfTilt Estimation]]

## [[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]] 

Appion is a "pipeline" for single particle reconstruction integrated with Leginon data acquisition. It consists of a web based user interface linked to a set of python scripts that control several underlying processing packages. These include EMAN, Spider, findem, ACE, and Chimera. All data input and output is managed by MySQL databases. The ultimate goal is to have all control of the processing pipeline managed from the web based user interface and all output from the processing presented using web based viewing tools. These notes are provided as a rough guide to using the pipeline but are not guaranteed to be up to date or accurate.

Appion users usually start off at a web page that presents them with a range of options for processing, reconstruction, analysis. This may have the following appearance:

The user can select to proceed with any of the steps but some of these may be dependent on earlier steps. For example a stack cannot be made until particles have been selected. After any of the steps has been run the user can chose to view the results by clicking on the "completed" or "available" labels. 

# [[Appion_scripts]]

# [[Appion_output]]

[[Administration Tools Guide]]

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[[Complete Installation|< Complete Installation]] | [[Upgrade Instructions|Upgrade Instructions >]]