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Appion Processing » History » Version 58

Sargis Dallakyan, 08/29/2014 12:04 PM

1 1 Amber Herold
h1. Appion Processing
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3 40 Amber Herold
## *[[Terminology]]*
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## *[[Common Workflow]]*
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*** [[Step by Step Guide]]
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*** [[Quality Assessment]]
7 49 Dmitry Lyumkis
*** [[Random-Conical Tilt (RCT) Reconstruction workflow]]
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*** [[Trimer Processing workflow]]
9 40 Amber Herold
## *[[Processing Cluster Login]]*
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## *[[Particle Selection]]*
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*** [[Template Picking]]
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*** [[Dog Picking]]
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*** [[Manual Picking]] 
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*** [[Repeat from other session]]
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*** [[Random Conical Tilt Picking]]
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**** [[Align and Edit Tilt Pairs]]
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**** [[Auto Align Tilt Pairs]]
18 40 Amber Herold
## *[[CTF Estimation]]* 
19 38 Anke Mulder
*** [[Ace Estimation]]
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*** [[Ace 2 Estimation]]
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*** [[CtfFind Estimation]]
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*** [[Repeat from other session]]
23 40 Amber Herold
## *[[Stacks]]* 
24 38 Anke Mulder
*** [[Stack creation]]
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*** [[more stack tools]]
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**** [[Combine Stacks]]
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**** [[View Stacks]] 
28 31 Anke Mulder
***** [[Filter by MeanSTDev]]
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***** [[Center Particles]]
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***** [[Sort Junk]]
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***** [[Create Substack]]
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**** [[Alignment SubStacks]]
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**** [[Jumpers SubStack]]
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**** [[Convert Stack into Particle Picks]]
35 40 Amber Herold
## *[[Particle Alignment]]* 
36 3 Anke Mulder
### [[Run Alignment]]
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**** [[Xmipp Maximum Likelihood Alignment]]
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**** [[Spider Reference-free Alignment]]
39 42 Dmitry Lyumkis
**** [[IMAGIC Multi Reference Alignment]]
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**** [[Spider Reference-based Alignment]]
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**** [[Ed's Iteration Alignment]]
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**** [[Xmipp Reference-based Maximum Likelihood Alignment]]
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**** [[Xmipp 3 Clustering 2D Alignment]]
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**** [[ISAC Iterative Stable Alignment and Clustering]]
45 36 Anke Mulder
### [[Run Feature Analysis]]
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**** [[Spider Coran Classification]]
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**** [[Xmipp Kerden Self-Organizing Map]]
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**** [[IMAGIC Multivariate Statistical Analysis (MSA)]]
49 3 Anke Mulder
**** [[Xmipp Rotational Kerden Self-Organizing Map]]
50 45 Amber Herold
**** [[Cluster by Affinity Propogation]]
51 3 Anke Mulder
### [[Run Particle Clustering]]
52 40 Amber Herold
## *[[Ab Initio Reconstruction]]*
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*** [[RCT Volume]] 
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*** [[OTR Volume]] 
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*** [[EMAN Common Lines]] 
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*** [[IMAGIC Angular Reconstitution]] 
57 40 Amber Herold
## *[[Refine Reconstruction]]* 
58 38 Anke Mulder
*** [[EMAN Refinement]]
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*** [[Frealign Refinement]]
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*** [[SPIDER Refinement]]
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*** [[IMAGIC Refinement]]
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*** [[Refinement Post-processing Procedures]]
63 47 Lauren Fisher
## *[[Helical Processing]]* 
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*** [[Helical Image Processing (PHOELIX)]]
65 40 Amber Herold
## *[[Tomography]]*
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### [[Align tilt series]]
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### [[Create full tomogram]]
68 39 Anke Mulder
### [[Upload_full_tomogram|Upload tomogram]]
69 17 Anke Mulder
### [[Create tomogram subvolume]]
70 44 Anchi Cheng
### [[Average tomogram subvolumes]]
71 40 Amber Herold
## *[[Import Tools]]* 
72 38 Anke Mulder
*** [[PDB to Model]]
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*** [[EMDB to Model]]
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*** [[Upload Particles]]
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*** [[Upload Template]]
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*** [[Upload Model]]
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*** [[Upload More Images]]
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*** [[Upload Stack]]
79 48 Dmitry Lyumkis
*** [[Upload Refinement]]
80 40 Amber Herold
## *[[Image Assessment]]* 
81 38 Anke Mulder
*** [[Web Img Assessment]]
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*** [[Multi Img Assessment]]
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*** [[Run Image Rejector]]
84 40 Amber Herold
## *[[Region Mask Creation]]*
85 38 Anke Mulder
*** [[Manual Masking]] 
86 50 Amber Herold
*** [[Maskiton]] 
87 40 Amber Herold
## *[[Synthetic Data]]* 
88 38 Anke Mulder
*** [[Synthetic Dataset Creation]]
89 51 Anchi Cheng
## *[[Direct Detector Frame Processing]]*
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*** [[Gain/Dark correction of the raw frame with or without drift correction]]
91 52 Anchi Cheng
*** [[Catch up DD frame alignment]] on gpu-capable processing host
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!http://emg.nysbc.org/attachments/282/Picture_83.png!
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!http://emg.nysbc.org/attachments/277/Picture_81.png!
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[[Appion and Leginon Database Tools|< Appion and Leginon Database Tools]]
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