Appion Processing¶

1. Terminology
2. Common Workflow
   1. Step by Step Guide
   2. Quality Assessment
3. Processing Cluster Login
4. Particle Selection
   1. Template Picking
   2. Dog Picking
   3. Manual Picking
   4. Repeat from other session
   5. Random Conical Tilt Picking
      1. Align and Edit Tilt Pairs
      2. Auto Align Tilt Pairs
5. CTF Estimation
   1. Ace Estimation
   2. Ace 2 Estimation
   3. CtfFind Estimation
   4. Repeat from other session
6. Stacks
   1. Stack creation
   2. more stack tools
7. Particle Alignment
   1. Run Alignment
   2. Run Feature Analysis
   3. Run Particle Clustering
8. Ab Initio Reconstruction
   1. RCT Volume
   2. OTR Volume
   3. EMAN Common Lines
   4. IMAGIC Angular Reconstitution
9. Refine Reconstruction
   1. EMAN Refinement
   2. Frealign Refinement
   3. SPIDER Refinement
   4. IMAGIC Refinement
10. Tomography
    1. Align tilt series
    2. Create full tomogram
    3. Upload tomogram
    4. Create tomogram subvolume
    5. Average subvolumes
11. Import Tools
    1. PDB to Model
    2. EMDB to Model
    3. Upload Particles
    4. Upload Template
    5. Upload Model
    6. Upload More Images
    7. Upload Stack
12. Image Assessment
    1. Web Img Assessment
    2. Multi Img Assessment
    3. Run Image Rejector
13. Region Mask Creation
    1. Manual Masking
14. Synthetic Data
    1. Synthetic Dataset Creation

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