Appion Manual¶

1. An Introduction to Appion
   1. What is Appion?
   2. System Requirements
   3. Authors
2. Complete Installation
   1. Instructions for installing CentOS on your computer
   2. Download additional Software
   3. Database Server Installation
   4. Processing Server Installation
   5. Web Server Installation
   6. Create a Test Project
   7. Setup Remote Processing
3. Upgrade Instructions
4. Appion User Guide
   1. Appion and Leginon Database Tools
      1. Administration
      2. User Management
      3. Project DB
      4. Image Viewers
      5. LOI - Leginon Observer Interface
      6. RCT
      7. Tomography
      8. Hole Template Viewer
   2. Appion Processing
      1. Terminology
      2. Common Workflow
      3. Processing Cluster Login
      4. Particle Selection
         1. Template Picking
         2. Dog Picking
         3. Manual Picking
      5. CTF Estimation
         1. Ace Estimation
         2. Ace 2 Estimation
         3. CtfTilt Estimation
      6. Import Tools
         1. PDB tp Model
         2. EMDB to Model
         3. Upload Particles
         4. Upload Template
         5. Upload Model
         6. Upload More Images
         7. Upload Stack
      7. Image Assessment
         1. Web Img Assessment
         2. Multi Img Assessment
         3. Run Image Rejector
      8. Region Mask Creation
         1. Crud Finding
         2. Manual Masking