Appion Processing » History » Revision 66
Revision 65 (Anchi Cheng, 11/12/2015 02:44 PM) → Revision 66/69 (Anchi Cheng, 11/12/2015 02:51 PM)
h1. Appion Processing ## *[[Terminology]]* ## *[[Common Workflow]]* *** [[Step by Step Guide]] *** [[Quality Assessment]] *** [[Random-Conical Tilt (RCT) Reconstruction workflow]] *** [[Trimer Processing workflow]] ## *[[Processing Cluster Login]]* ## *[[Particle Selection]]* *** [[Template Picking]] *** [[Dog Picking]] *** [[Manual Picking]] *** [[Repeat from other session]] *** [[Random Conical Tilt Picking]] **** [[Align and Edit Tilt Pairs]] **** [[Auto Align Tilt Pairs]] ## *[[CTF Estimation]]* *** [[Ace Estimation]] *** [[Ace 2 Estimation]] *** [[CtfFind Estimation]] *** [[Repeat from other session]] ## *[[Stacks]]* *** [[Stack creation]] *** [[more stack tools]] **** [[Combine Stacks]] **** [[View Stacks]] ***** [[Filter by MeanSTDev]] ***** [[Center Particles]] ***** [[Sort Junk]] ***** [[Create Substack]] **** [[Alignment SubStacks]] **** [[Jumpers SubStack]] **** [[Convert Stack into Particle Picks]] **** [[Run DE Particle Frame Alignment]] ## *[[Particle Alignment]]* ### [[Run Alignment]] **** [[Xmipp Maximum Likelihood Alignment]] **** [[Spider Reference-free Alignment]] **** [[IMAGIC Multi Reference Alignment]] **** [[Spider Reference-based Alignment]] **** [[Ed's Iteration Alignment]] **** [[Xmipp Reference-based Maximum Likelihood Alignment]] **** [[Xmipp 3 Clustering 2D Alignment]] **** [[ISAC Iterative Stable Alignment and Clustering]] ### [[Run Feature Analysis]] **** [[Spider Coran Classification]] **** [[Xmipp Kerden Self-Organizing Map]] **** [[IMAGIC Multivariate Statistical Analysis (MSA)]] **** [[Xmipp Rotational Kerden Self-Organizing Map]] **** [[Cluster by Affinity Propogation]] ### [[Run Particle Clustering]] ## *[[Ab Initio Reconstruction]]* *** [[RCT Volume]] *** [[OTR Volume]] *** [[EMAN Common Lines]] *** [[IMAGIC Angular Reconstitution]] ## *[[Refine Reconstruction]]* *** [[EMAN Refinement]] *** [[Frealign Refinement]] *** [[SPIDER Refinement]] *** [[IMAGIC Refinement]] *** [[Refinement Post-processing Procedures]] ## *[[Helical Processing]]* *** Manual Helix Picker Feature #1771 ## *[[Tomography]]* *** [[Align Tilt Series|Auto align+reconstruction]] *** [[Align Tilt-Series|Align Tilt-Series (Appion-Protomo)]] *** [[Upload full tomogram|Create & Upload Tomogram]] *** [[Create tomogram subvolume|Create Tomogram Subvolume]] *** [[Average tomogram subvolumes|Average Subvolumes]] ## *[[Import Tools]]* *** [[PDB to Model]] *** [[EMDB to Model]] *** [[Upload Particles]] *** [[Upload Template]] *** [[Upload Model]] *** [[Upload More Images]] ( or see [[Upload Images]][[Upload Images to a new Project Session]] ) *** [[Upload Stack]] *** [[Upload Refinement]] ## *[[Image Assessment]]* *** [[Web Img Assessment]] *** [[Multi Img Assessment]] *** [[Run Image Rejector]] ## *[[Region Mask Creation]]* *** [[Manual Masking]] *** [[Maskiton]] ## *[[Synthetic Data]]* *** [[Synthetic Dataset Creation]] ## *[[Direct Detector Frame Processing]]* *** [[Gain/Dark correction of the raw frame with or without drift correction]] *** [[Catch up DD frame alignment]] on gpu-capable processing host !http://emg.nysbc.org/attachments/282/Picture_83.png! !http://emg.nysbc.org/attachments/277/Picture_81.png! ______ [[Appion and Leginon Database Tools|< Appion and Leginon Database Tools]] ______