Appion Processing » History » Version 62
Anchi Cheng, 05/12/2015 11:40 AM
1 | 1 | Amber Herold | h1. Appion Processing |
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2 | |||
3 | 40 | Amber Herold | ## *[[Terminology]]* |
4 | ## *[[Common Workflow]]* |
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5 | 38 | Anke Mulder | *** [[Step by Step Guide]] |
6 | *** [[Quality Assessment]] |
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7 | 49 | Dmitry Lyumkis | *** [[Random-Conical Tilt (RCT) Reconstruction workflow]] |
8 | 55 | Dmitry Lyumkis | *** [[Trimer Processing workflow]] |
9 | 40 | Amber Herold | ## *[[Processing Cluster Login]]* |
10 | 41 | Amber Herold | ## *[[Particle Selection]]* |
11 | 38 | Anke Mulder | *** [[Template Picking]] |
12 | *** [[Dog Picking]] |
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13 | *** [[Manual Picking]] |
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14 | *** [[Repeat from other session]] |
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15 | *** [[Random Conical Tilt Picking]] |
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16 | 32 | Anke Mulder | **** [[Align and Edit Tilt Pairs]] |
17 | **** [[Auto Align Tilt Pairs]] |
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18 | 40 | Amber Herold | ## *[[CTF Estimation]]* |
19 | 38 | Anke Mulder | *** [[Ace Estimation]] |
20 | *** [[Ace 2 Estimation]] |
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21 | *** [[CtfFind Estimation]] |
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22 | *** [[Repeat from other session]] |
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23 | 40 | Amber Herold | ## *[[Stacks]]* |
24 | 38 | Anke Mulder | *** [[Stack creation]] |
25 | *** [[more stack tools]] |
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26 | **** [[Combine Stacks]] |
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27 | **** [[View Stacks]] |
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28 | 31 | Anke Mulder | ***** [[Filter by MeanSTDev]] |
29 | ***** [[Center Particles]] |
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30 | ***** [[Sort Junk]] |
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31 | 33 | Anke Mulder | ***** [[Create Substack]] |
32 | 38 | Anke Mulder | **** [[Alignment SubStacks]] |
33 | 58 | Sargis Dallakyan | **** [[Jumpers SubStack]] |
34 | 38 | Anke Mulder | **** [[Convert Stack into Particle Picks]] |
35 | 59 | Amber Herold | **** [[Run DE Particle Frame Alignment]] |
36 | 40 | Amber Herold | ## *[[Particle Alignment]]* |
37 | 3 | Anke Mulder | ### [[Run Alignment]] |
38 | 34 | Anke Mulder | **** [[Xmipp Maximum Likelihood Alignment]] |
39 | **** [[Spider Reference-free Alignment]] |
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40 | 42 | Dmitry Lyumkis | **** [[IMAGIC Multi Reference Alignment]] |
41 | 34 | Anke Mulder | **** [[Spider Reference-based Alignment]] |
42 | **** [[Ed's Iteration Alignment]] |
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43 | **** [[Xmipp Reference-based Maximum Likelihood Alignment]] |
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44 | 57 | Amber Herold | **** [[Xmipp 3 Clustering 2D Alignment]] |
45 | 56 | Sargis Dallakyan | **** [[ISAC Iterative Stable Alignment and Clustering]] |
46 | 36 | Anke Mulder | ### [[Run Feature Analysis]] |
47 | **** [[Spider Coran Classification]] |
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48 | **** [[Xmipp Kerden Self-Organizing Map]] |
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49 | 45 | Amber Herold | **** [[IMAGIC Multivariate Statistical Analysis (MSA)]] |
50 | 3 | Anke Mulder | **** [[Xmipp Rotational Kerden Self-Organizing Map]] |
51 | 45 | Amber Herold | **** [[Cluster by Affinity Propogation]] |
52 | 3 | Anke Mulder | ### [[Run Particle Clustering]] |
53 | 40 | Amber Herold | ## *[[Ab Initio Reconstruction]]* |
54 | 38 | Anke Mulder | *** [[RCT Volume]] |
55 | *** [[OTR Volume]] |
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56 | *** [[EMAN Common Lines]] |
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57 | *** [[IMAGIC Angular Reconstitution]] |
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58 | 40 | Amber Herold | ## *[[Refine Reconstruction]]* |
59 | 38 | Anke Mulder | *** [[EMAN Refinement]] |
60 | *** [[Frealign Refinement]] |
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61 | *** [[SPIDER Refinement]] |
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62 | *** [[IMAGIC Refinement]] |
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63 | 43 | Amber Herold | *** [[Refinement Post-processing Procedures]] |
64 | 47 | Lauren Fisher | ## *[[Helical Processing]]* |
65 | 62 | Anchi Cheng | *** Manual Helix Picker Feature #1771 |
66 | 40 | Amber Herold | ## *[[Tomography]]* |
67 | 17 | Anke Mulder | ### [[Align tilt series]] |
68 | ### [[Create full tomogram]] |
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69 | 39 | Anke Mulder | ### [[Upload_full_tomogram|Upload tomogram]] |
70 | 17 | Anke Mulder | ### [[Create tomogram subvolume]] |
71 | 44 | Anchi Cheng | ### [[Average tomogram subvolumes]] |
72 | 40 | Amber Herold | ## *[[Import Tools]]* |
73 | 38 | Anke Mulder | *** [[PDB to Model]] |
74 | *** [[EMDB to Model]] |
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75 | *** [[Upload Particles]] |
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76 | *** [[Upload Template]] |
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77 | *** [[Upload Model]] |
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78 | *** [[Upload More Images]] |
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79 | *** [[Upload Stack]] |
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80 | 48 | Dmitry Lyumkis | *** [[Upload Refinement]] |
81 | 40 | Amber Herold | ## *[[Image Assessment]]* |
82 | 38 | Anke Mulder | *** [[Web Img Assessment]] |
83 | *** [[Multi Img Assessment]] |
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84 | *** [[Run Image Rejector]] |
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85 | 40 | Amber Herold | ## *[[Region Mask Creation]]* |
86 | 38 | Anke Mulder | *** [[Manual Masking]] |
87 | 50 | Amber Herold | *** [[Maskiton]] |
88 | 40 | Amber Herold | ## *[[Synthetic Data]]* |
89 | 38 | Anke Mulder | *** [[Synthetic Dataset Creation]] |
90 | 51 | Anchi Cheng | ## *[[Direct Detector Frame Processing]]* |
91 | *** [[Gain/Dark correction of the raw frame with or without drift correction]] |
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92 | 52 | Anchi Cheng | *** [[Catch up DD frame alignment]] on gpu-capable processing host |
93 | 22 | Anke Mulder | |
94 | !http://emg.nysbc.org/attachments/282/Picture_83.png! |
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95 | 19 | Anke Mulder | !http://emg.nysbc.org/attachments/277/Picture_81.png! |
96 | 22 | Anke Mulder | |
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100 | 5 | Amber Herold | |
101 | 2 | Amber Herold | ______ |
102 | |||
103 | [[Appion and Leginon Database Tools|< Appion and Leginon Database Tools]] |
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104 | |||
105 | ______ |