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
      1. Install supporting packages
      2. Download Appion Files
      3. Perform system check
      4. Install Appion Packages
      5. Configure leginon.cfg
      6. Explanation of Sample Names
      7. Configure sinedon.cfg
      8. Install External Packages
      9. Compile FindEM
      10. Compile Ace2
      11. Compile Radermacher
      12. Install Xmipp
      13. Test Appion
   5. Web Server Installation
      1. Differences between Linux flavors
      2. Install Web Server Prerequisites
      3. Configure php.ini
      4. Install Apache Web Server
      5. Check php information
      6. Install the MRC PHP Extension
      7. Install the Web Interface
      8. Potential Problems
   6. Create a Test Project
   7. Setup Remote Processing
3. Upgrade Instructions
4. Appion User Guide
   1. Appion and Leginon Database Tools
      1. Administration
         1. Groups
         2. Users
         3. Instruments
         4. Default Settings
         5. Calibrations
         6. Applications
         7. Goniometer
      2. User Management
         1. Enable User Authentication
         2. New User Registration
         3. Retrieve Forgotten Password
         4. Modify Your Profile
         5. Logout
      3. Project DB
         1. View Projects
         2. Create New Project
         3. Edit Project Description
         4. Edit Project Owners
         5. Create a Project Processing Database
         6. Unlink a Project Processing Database
         7. Upload Images to a new Project Session
         8. Share a Project Session with another User
         9. View a Summary of a Project Session
         10. Grid Management
      4. Image Viewers
         1. Image Viewer
         2. 2 Way Viewer
         3. 3 Way Viewer
         4. Dual Viewer
         5. Image Tools
      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