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Appion Processing » History » Version 40

Amber Herold, 07/29/2010 02:00 PM

1 1 Amber Herold 
h1. Appion Processing
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## *[[Terminology]]*





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## *[[Common Workflow]]*





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*** [[Step by Step Guide]]





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*** [[Quality Assessment]]





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## *[[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]]





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## *[[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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**** [[ Jumpers SubStack]]





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**** [[Convert Stack into Particle Picks]]





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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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**** [[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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### [[Run Feature Analysis]]





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**** [[Spider Coran Classification]]





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**** [[Xmipp Kerden Self-Organizing Map]]





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**** [[Xmipp Rotational Kerden Self-Organizing Map]]





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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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## *[[Tomography]]*





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### [[Align tilt series]]





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### [[Create full tomogram]]





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### [[Upload_full_tomogram|Upload tomogram]]





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### [[Create tomogram subvolume]]





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### [[Average subvolumes]]





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## *[[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]]





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*** [[Upload Stack]]





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## *[[Image Assessment]]* 





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*** [[Web Img Assessment]]





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*** [[Multi Img Assessment]]





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*** [[Run Image Rejector]]





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## *[[Region Mask Creation]]*





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*** [[Manual Masking]] 





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## *[[Synthetic Data]]* 





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*** [[Synthetic Dataset Creation]]





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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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