Appion Processing » History » Version 38
Anke Mulder, 06/14/2010 12:20 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 | 38 | 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 | 38 | Anke Mulder | *** [[Template Picking]] |
| 10 | *** [[Dog Picking]] |
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| 11 | *** [[Manual Picking]] |
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| 12 | *** [[Repeat from other session]] |
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| 13 | *** [[Random Conical Tilt Picking]] |
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| 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 | 38 | Anke Mulder | *** [[Ace Estimation]] |
| 18 | *** [[Ace 2 Estimation]] |
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| 19 | *** [[CtfFind Estimation]] |
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| 20 | *** [[Repeat from other session]] |
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| 21 | 20 | Anke Mulder | ## [[Stacks]] |
| 22 | 38 | Anke Mulder | *** [[Stack creation]] |
| 23 | *** [[more stack tools]] |
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| 24 | **** [[Combine Stacks]] |
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| 25 | **** [[View Stacks]] |
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| 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 | 38 | Anke Mulder | **** [[Alignment SubStacks]] |
| 31 | **** [[ Jumpers SubStack]] |
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| 32 | **** [[Convert Stack into Particle Picks]] |
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| 33 | 20 | Anke Mulder | ## [[Particle Alignment]] |
| 34 | 3 | Anke Mulder | ### [[Run Alignment]] |
| 35 | 34 | Anke Mulder | **** [[Xmipp Maximum Likelihood Alignment]] |
| 36 | **** [[Spider Reference-free Alignment]] |
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| 37 | **** [[Spider Reference-based Alignment]] |
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| 38 | **** [[Ed's Iteration Alignment]] |
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| 39 | **** [[Xmipp Reference-based Maximum Likelihood Alignment]] |
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| 40 | 36 | Anke Mulder | ### [[Run Feature Analysis]] |
| 41 | **** [[Spider Coran Classification]] |
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| 42 | **** [[Xmipp Kerden Self-Organizing Map]] |
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| 43 | 3 | Anke Mulder | **** [[Xmipp Rotational Kerden Self-Organizing Map]] |
| 44 | ### [[Run Particle Clustering]] |
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| 45 | 20 | Anke Mulder | ## [[Ab Initio Reconstruction]] |
| 46 | 38 | Anke Mulder | *** [[RCT Volume]] |
| 47 | *** [[OTR Volume]] |
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| 48 | *** [[EMAN Common Lines]] |
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| 49 | *** [[IMAGIC Angular Reconstitution]] |
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| 50 | 3 | Anke Mulder | ## [[Refine Reconstruction]] |
| 51 | 38 | Anke Mulder | *** [[EMAN Refinement]] |
| 52 | *** [[Frealign Refinement]] |
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| 53 | *** [[SPIDER Refinement]] |
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| 54 | *** [[IMAGIC Refinement]] |
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| 55 | 17 | Anke Mulder | ## [[Tomography]] |
| 56 | ### [[Align tilt series]] |
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| 57 | ### [[Create full tomogram]] |
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| 58 | ### [[Upload tomogram]] |
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| 59 | ### [[Create tomogram subvolume]] |
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| 60 | 20 | Anke Mulder | ### [[Average subvolumes]] |
| 61 | 6 | Pick-Wei Lau | ## [[Import Tools]] |
| 62 | 38 | Anke Mulder | *** [[PDB to Model]] |
| 63 | *** [[EMDB to Model]] |
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| 64 | *** [[Upload Particles]] |
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| 65 | *** [[Upload Template]] |
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| 66 | *** [[Upload Model]] |
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| 67 | *** [[Upload More Images]] |
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| 68 | *** [[Upload Stack]] |
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| 69 | 1 | Amber Herold | ## [[Image Assessment]] |
| 70 | 38 | Anke Mulder | *** [[Web Img Assessment]] |
| 71 | *** [[Multi Img Assessment]] |
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| 72 | *** [[Run Image Rejector]] |
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| 73 | 1 | Amber Herold | ## [[Region Mask Creation]] |
| 74 | 38 | Anke Mulder | *** [[Manual Masking]] |
| 75 | 1 | Amber Herold | ## [[Synthetic Data]] |
| 76 | 38 | Anke Mulder | *** [[Synthetic Dataset Creation]] |
| 77 | 37 | Anke Mulder | |
| 78 | 22 | Anke Mulder | |
| 79 | !http://emg.nysbc.org/attachments/282/Picture_83.png! |
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| 80 | 19 | Anke Mulder | !http://emg.nysbc.org/attachments/277/Picture_81.png! |
| 81 | 22 | Anke Mulder | |
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| 85 | 5 | Amber Herold | |
| 86 | 2 | Amber Herold | ______ |
| 87 | |||
| 88 | [[Appion and Leginon Database Tools|< Appion and Leginon Database Tools]] |
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| 89 | |||
| 90 | ______ |