Appion Processing » History » Version 34
Anke Mulder, 06/14/2010 12:14 PM
| 1 | 1 | Amber Herold | h1. Appion Processing |
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| 2 | |||
| 3 | ## [[Terminology]] |
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| 4 | 10 | Anke Mulder | ## [[Common Workflow]] |
| 5 | 8 | Anke Mulder | ### [[Step by Step Guide]] |
| 6 | ### [[Quality Assessment]] |
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| 7 | 1 | Amber Herold | ## [[Processing Cluster Login]] |
| 8 | 20 | Anke Mulder | ## [[Particle Selection]] |
| 9 | 1 | Amber Herold | ### [[Template Picking]] |
| 10 | ### [[Dog Picking]] |
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| 11 | ### [[Manual Picking]] |
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| 12 | 3 | Anke Mulder | ### [[Repeat from other session]] |
| 13 | 24 | Anke Mulder | ### [[Random Conical Tilt Picking]] |
| 14 | 32 | Anke Mulder | **** [[Align and Edit Tilt Pairs]] |
| 15 | **** [[Auto Align Tilt Pairs]] |
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| 16 | 20 | Anke Mulder | ## [[CTF Estimation]] |
| 17 | 1 | Amber Herold | ### [[Ace Estimation]] |
| 18 | ### [[Ace 2 Estimation]] |
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| 19 | 16 | Anke Mulder | ### [[CtfFind Estimation]] |
| 20 | 3 | Anke Mulder | ### [[Repeat from other session]] |
| 21 | 20 | Anke Mulder | ## [[Stacks]] |
| 22 | 3 | Anke Mulder | ### [[Stack creation]] |
| 23 | ### [[more stack tools]] |
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| 24 | 26 | Anke Mulder | #### [[Combine Stacks]] |
| 25 | 30 | Anke Mulder | #### [[View Stacks]] |
| 26 | 31 | Anke Mulder | ***** [[Filter by MeanSTDev]] |
| 27 | ***** [[Center Particles]] |
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| 28 | ***** [[Sort Junk]] |
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| 29 | 33 | Anke Mulder | ***** [[Create Substack]] |
| 30 | 26 | Anke Mulder | #### [[Alignment SubStacks]] |
| 31 | #### [[ Jumpers SubStack]] |
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| 32 | #### [[Convert Stack into Particle Picks]] |
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| 33 | |||
| 34 | 20 | Anke Mulder | ## [[Particle Alignment]] |
| 35 | 3 | Anke Mulder | ### [[Run Alignment]] |
| 36 | 34 | Anke Mulder | **** [[Xmipp Maximum Likelihood Alignment]] |
| 37 | **** [[Spider Reference-free Alignment]] |
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| 38 | **** [[Spider Reference-based Alignment]] |
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| 39 | **** [[Ed's Iteration Alignment]] |
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| 40 | **** [[Xmipp Reference-based Maximum Likelihood Alignment]] |
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| 41 | |||
| 42 | 3 | Anke Mulder | ### [[Run Feature Analysis]] |
| 43 | ### [[Run Particle Clustering]] |
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| 44 | ## [[Ab Initio Reconstruction]] |
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| 45 | 20 | Anke Mulder | ### [[RCT Volume]] |
| 46 | ### [[OTR Volume]] |
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| 47 | ### [[EMAN Common Lines]] |
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| 48 | 4 | Anke Mulder | ### [[IMAGIC Angular Reconstitution]] |
| 49 | 20 | Anke Mulder | ## [[Refine Reconstruction]] |
| 50 | 3 | Anke Mulder | ### [[EMAN Refinement]] |
| 51 | 14 | Anke Mulder | ### [[Frealign Refinement]] |
| 52 | 25 | Anke Mulder | ### [[SPIDER Refinement]] |
| 53 | ### [[IMAGIC Refinement]] |
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| 54 | 15 | Anke Mulder | ## [[Tomography]] |
| 55 | 17 | Anke Mulder | ### [[Align tilt series]] |
| 56 | ### [[Create full tomogram]] |
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| 57 | ### [[Upload tomogram]] |
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| 58 | ### [[Create tomogram subvolume]] |
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| 59 | ### [[Average subvolumes]] |
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| 60 | 20 | Anke Mulder | ## [[Import Tools]] |
| 61 | 6 | Pick-Wei Lau | ### [[PDB to Model]] |
| 62 | 1 | Amber Herold | ### [[EMDB to Model]] |
| 63 | ### [[Upload Particles]] |
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| 64 | ### [[Upload Template]] |
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| 65 | ### [[Upload Model]] |
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| 66 | ### [[Upload More Images]] |
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| 67 | ### [[Upload Stack]] |
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| 68 | 20 | Anke Mulder | ## [[Image Assessment]] |
| 69 | 1 | Amber Herold | ### [[Web Img Assessment]] |
| 70 | ### [[Multi Img Assessment]] |
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| 71 | ### [[Run Image Rejector]] |
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| 72 | 20 | Anke Mulder | ## [[Region Mask Creation]] |
| 73 | 1 | Amber Herold | ### [[Manual Masking]] |
| 74 | 20 | Anke Mulder | ## [[Synthetic Data]] |
| 75 | 1 | Amber Herold | ### [[Synthetic Dataset Creation]] |
| 76 | 19 | Anke Mulder | |
| 77 | 22 | Anke Mulder | |
| 78 | !http://emg.nysbc.org/attachments/282/Picture_83.png! |
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| 79 | 19 | Anke Mulder | !http://emg.nysbc.org/attachments/277/Picture_81.png! |
| 80 | 22 | Anke Mulder | |
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| 84 | 5 | Amber Herold | |
| 85 | 2 | Amber Herold | ______ |
| 86 | |||
| 87 | [[Appion and Leginon Database Tools|< Appion and Leginon Database Tools]] |
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| 88 | |||
| 89 | ______ |