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Appion Processing » History » Version 60

Anchi Cheng, 05/12/2015 11:36 AM

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]]* 
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*** [[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]]* 
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*** [[Stack creation]]
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*** [[more stack tools]]
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**** [[Combine Stacks]]
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**** [[View Stacks]] 
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***** [[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]]
33 58 Sargis Dallakyan
**** [[Jumpers SubStack]]
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**** [[Convert Stack into Particle Picks]]
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**** [[Run DE Particle Frame Alignment]]
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## *[[Particle Alignment]]* 
37 3 Anke Mulder
### [[Run Alignment]]
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**** [[Xmipp Maximum Likelihood Alignment]]
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**** [[Spider Reference-free Alignment]]
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**** [[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]]
45 56 Sargis Dallakyan
**** [[ISAC Iterative Stable Alignment and Clustering]]
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### [[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)]]
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**** [[Xmipp Rotational Kerden Self-Organizing Map]]
51 45 Amber Herold
**** [[Cluster by Affinity Propogation]]
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### [[Run Particle Clustering]]
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## *[[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]] 
58 40 Amber Herold
## *[[Refine Reconstruction]]* 
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*** [[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]]
64 47 Lauren Fisher
## *[[Helical Processing]]* 
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*** [[#1771|Manual]]
66 40 Amber Herold
## *[[Tomography]]*
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### [[Align tilt series]]
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### [[Create full tomogram]]
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]]
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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]]
80 48 Dmitry Lyumkis
*** [[Upload Refinement]]
81 40 Amber Herold
## *[[Image Assessment]]* 
82 38 Anke Mulder
*** [[Web Img Assessment]]
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*** [[Multi Img Assessment]]
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*** [[Run Image Rejector]]
85 40 Amber Herold
## *[[Region Mask Creation]]*
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*** [[Manual Masking]] 
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*** [[Maskiton]] 
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## *[[Synthetic Data]]* 
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*** [[Synthetic Dataset Creation]]
90 51 Anchi Cheng
## *[[Direct Detector Frame Processing]]*
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*** [[Gain/Dark correction of the raw frame with or without drift correction]]
92 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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