Test page » History » Version 1
Anke Mulder, 06/14/2010 12:18 PM
| 1 | 1 | Anke Mulder | h1. Appion Processing |
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| 2 | |||
| 3 | ## [[Terminology]] |
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| 4 | ## [[Common Workflow]] |
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| 5 | *** [[Step by Step Guide]] |
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| 6 | *** [[Quality Assessment]] |
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| 7 | ## [[Processing Cluster Login]] |
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| 8 | ## [[Particle Selection]] |
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| 9 | *** [[Template Picking]] |
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| 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 | **** [[Align and Edit Tilt Pairs]] |
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| 15 | **** [[Auto Align Tilt Pairs]] |
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| 16 | ## [[CTF Estimation]] |
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| 17 | *** [[Ace Estimation]] |
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| 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 | ## [[Stacks]] |
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| 22 | *** [[Stack creation]] |
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| 23 | *** [[more stack tools]] |
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| 24 | **** [[Combine Stacks]] |
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| 25 | **** [[View Stacks]] |
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| 26 | ***** [[Filter by MeanSTDev]] |
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| 27 | ***** [[Center Particles]] |
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| 28 | ***** [[Sort Junk]] |
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| 29 | ***** [[Create Substack]] |
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| 30 | **** [[Alignment SubStacks]] |
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| 31 | **** [[ Jumpers SubStack]] |
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| 32 | **** [[Convert Stack into Particle Picks]] |
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| 33 | ## [[Particle Alignment]] |
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| 34 | ### [[Run Alignment]] |
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| 35 | **** [[Xmipp Maximum Likelihood Alignment]] |
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| 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 | ### [[Run Feature Analysis]] |
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| 41 | **** [[Spider Coran Classification]] |
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| 42 | **** [[Xmipp Kerden Self-Organizing Map]] |
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| 43 | **** [[Xmipp Rotational Kerden Self-Organizing Map]] |
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| 44 | ### [[Run Particle Clustering]] |
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| 45 | ## [[Ab Initio Reconstruction]] |
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| 46 | *** [[RCT Volume]] |
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| 47 | *** [[OTR Volume]] |
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| 48 | *** [[EMAN Common Lines]] |
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| 49 | *** [[IMAGIC Angular Reconstitution]] |
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| 50 | ## [[Refine Reconstruction]] |
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| 51 | *** [[EMAN Refinement]] |
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| 52 | *** [[Frealign Refinement]] |
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| 53 | *** [[SPIDER Refinement]] |
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| 54 | *** [[IMAGIC Refinement]] |
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| 55 | ## [[Tomography]] |
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| 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 | ### [[Average subvolumes]] |
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| 61 | ## [[Import Tools]] |
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| 62 | *** [[PDB to Model]] |
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| 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 | ## [[Image Assessment]] |
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| 70 | *** [[Web Img Assessment]] |
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| 71 | *** [[Multi Img Assessment]] |
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| 72 | *** [[Run Image Rejector]] |
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| 73 | ## [[Region Mask Creation]] |
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| 74 | *** [[Manual Masking]] |
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| 75 | ## [[Synthetic Data]] |
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| 76 | *** [[Synthetic Dataset Creation]] |
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| 79 | !http://emg.nysbc.org/attachments/282/Picture_83.png! |
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| 80 | !http://emg.nysbc.org/attachments/277/Picture_81.png! |
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| 86 | ______ |
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| 87 | |||
| 88 | [[Appion and Leginon Database Tools|< Appion and Leginon Database Tools]] |
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| 89 | |||
| 90 | ______ |