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Appion Processing » History » Version 65

Anchi Cheng, 11/12/2015 02:44 PM

1 1 Amber Herold 
h1. Appion Processing
2 





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    Amber Herold
    
## *[[Terminology]]*





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## *[[Common Workflow]]*





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    Anke Mulder
    
*** [[Step by Step Guide]]





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*** [[Quality Assessment]]





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    Dmitry Lyumkis
    
*** [[Random-Conical Tilt (RCT) Reconstruction workflow]]





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    Dmitry Lyumkis
    
*** [[Trimer Processing workflow]]





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    Amber Herold
    
## *[[Processing Cluster Login]]*





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    Amber Herold
    
## *[[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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    Anke Mulder
    
**** [[Align and Edit Tilt Pairs]]





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**** [[Auto Align Tilt Pairs]]





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    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]]





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## *[[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]]





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    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]]* 





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### [[Run Alignment]]





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**** [[Xmipp Maximum Likelihood Alignment]]





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**** [[Spider Reference-free Alignment]]





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    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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    Amber Herold
    
**** [[Xmipp 3 Clustering 2D Alignment]]





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    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]]





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**** [[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]] 





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## *[[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]]





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    Lauren Fisher
    
## *[[Helical Processing]]* 





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    Anchi Cheng
    
*** Manual Helix Picker Feature #1771





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## *[[Tomography]]*





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    Alex Noble
    
*** [[Align Tilt Series|Auto align+reconstruction]]





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*** [[Align Tilt-Series|Align Tilt-Series (Appion-Protomo)]]





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*** [[Upload full tomogram|Create & Upload Tomogram]]





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*** [[Create tomogram subvolume|Create Tomogram Subvolume]]





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*** [[Average tomogram subvolumes|Average Subvolumes]]





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    Amber Herold
    
## *[[Import Tools]]* 





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*** [[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]][[Upload Images to a new Project Session]]





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*** [[Upload Stack]]





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    Dmitry Lyumkis
    
*** [[Upload Refinement]]





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    Amber Herold
    
## *[[Image Assessment]]* 





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    Anke Mulder
    
*** [[Web Img Assessment]]





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*** [[Multi Img Assessment]]





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*** [[Run Image Rejector]]





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    Amber Herold
    
## *[[Region Mask Creation]]*





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    Anke Mulder
    
*** [[Manual Masking]] 





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*** [[Maskiton]] 





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## *[[Synthetic Data]]* 





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    Anke Mulder
    
*** [[Synthetic Dataset Creation]]





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## *[[Direct Detector Frame Processing]]*





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*** [[Gain/Dark correction of the raw frame with or without drift correction]]





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*** [[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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