Appion

h1. Refine Reconstruction

Most initial models establish nothing more than a preliminary sense of the overall shape of the biological specimen. In order to reveal structural information that can answer specific biological questions, the model requires refining. In single particle analysis, a refinement is an iterative procedure, which sequentially aligns the raw particles, assign to them appropriate spatial orientations (Euler angles) by comparing them against the a model, and then back-projects them into 3D space to form a new model.  Effectively, a full refinement takes as input a raw particle stack and an initial model and is usually carried out until no further improvement of the structure can be observed, often measured by convergence to some resolution criterion.

h2. Refinement Options Available in Appion:

# [[EMAN_Refinement|EMAN Refinement]]

# [[Frealign_Refinement|Frealign Refinement]]

# [[SPIDER_Refinement|SPIDER Refinement]]

# [[IMAGIC_Refinement|IMAGIC Refinement]]

# [[Refinement Post-processing Procedures]]

h2. Appion Sidebar Snapshot:

!http://emg.nysbc.org/attachments/287/Picture_88.png!

h2. Notes, Comments, and Suggestions:

!http://emg.nysbc.org/attachments/282/Picture_83.png!

!http://emg.nysbc.org/attachments/277/Picture_81.png!

[[Reconstruction Parameters]]

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[[Ab Initio Reconstruction|< Ab Initio Reconstruction]]|[[Quality_Assessment|Quality Assessment >]] 

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