Appion Processing¶

1. Terminology
2. Common Workflow
   • Step by Step Guide
   • Quality Assessment
   • Random-Conical Tilt (RCT) Reconstruction workflow
   • Trimer Processing workflow
3. Processing Cluster Login
4. Particle Selection
   • Template Picking
   • Dog Picking
   • Manual Picking
   • Repeat from other session
   • Random Conical Tilt Picking
     • Align and Edit Tilt Pairs
     • Auto Align Tilt Pairs
5. CTF Estimation
   • Ace Estimation
   • Ace 2 Estimation
   • CtfFind Estimation
   • Repeat from other session
6. Stacks
   • Stack creation
   • more stack tools
     • Combine Stacks
     • View Stacks
       • Filter by MeanSTDev
       • Center Particles
       • Sort Junk
       • Create Substack
     • Alignment SubStacks
     • Jumpers SubStack
     • Convert Stack into Particle Picks
     • Run DE Particle Frame Alignment
7. Particle Alignment
   1. Run Alignment
      • Xmipp Maximum Likelihood Alignment
      • Spider Reference-free Alignment
      • IMAGIC Multi Reference Alignment
      • Spider Reference-based Alignment
      • Ed's Iteration Alignment
      • Xmipp Reference-based Maximum Likelihood Alignment
      • Xmipp 3 Clustering 2D Alignment
      • ISAC Iterative Stable Alignment and Clustering
   2. Run Feature Analysis
      • Spider Coran Classification
      • Xmipp Kerden Self-Organizing Map
      • IMAGIC Multivariate Statistical Analysis (MSA)
      • Xmipp Rotational Kerden Self-Organizing Map
      • Cluster by Affinity Propogation
   3. Run Particle Clustering
8. Ab Initio Reconstruction
   • RCT Volume
   • OTR Volume
   • EMAN Common Lines
   • IMAGIC Angular Reconstitution
9. Refine Reconstruction
   • EMAN Refinement
   • Frealign Refinement
   • SPIDER Refinement
   • IMAGIC Refinement
   • Refinement Post-processing Procedures
10. Helical Processing
    • Manual Helix Picker Feature #1771
11. Tomography
    1. Auto align+reconstruction
    2. Align Tilt-Series (Appion-Protomo)
    3. Create & Upload Tomogram
    4. Create Tomogram Subvolume
    5. Average Subvolumes
12. Import Tools
    • PDB to Model
    • EMDB to Model
    • Upload Particles
    • Upload Template
    • Upload Model
    • Upload More Images
    • Upload Stack
    • Upload Refinement
13. Image Assessment
    • Web Img Assessment
    • Multi Img Assessment
    • Run Image Rejector
14. Region Mask Creation
    • Manual Masking
    • Maskiton
15. Synthetic Data
    • Synthetic Dataset Creation
16. Direct Detector Frame Processing
    • Gain/Dark correction of the raw frame with or without drift correction
    • Catch up DD frame alignment on gpu-capable processing host

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