Difference between revisions of "Walkthrough on localized reconstruction"
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=== Geometric conventions === | === Geometric conventions === | ||
| − | In ''Dynamo'', we call ''stack 3d center'' to a point (x< | + | In ''Dynamo'', we call ''stack 3d center'' to a point (x<sub>sc</sub>, y<sub>sc</sub>,z<sub>sc</sub> ) univocally defined by a stack of micrographs: |
| − | * ''x'' and ''z'' and determined by the rotation axis implicitly defined by the alignment. | + | * ''x<sub>sc</sub>'' and ''z'' and determined by the rotation axis implicitly defined by the alignment. |
* ''y'' is the center of the stack along direction ''y'', defined as | * ''y'' is the center of the stack along direction ''y'', defined as | ||
Revision as of 16:40, 31 October 2017
ARTICLE IN CONSTRUCTION, SORRY
In this walkthrough, we use localized reconstruction to reconstruct a set of subtomograms at full pixel resolution without the requirement of creating a full reconstruction first. In this approach, we:
- create a reconstruction at low resolution
- mark the coordinates of interest in the low resolution reconstruction
- reconstruct separately the different coordinates.
Contents
Example data set
The data set is an aligned tilt series.
Source
The tilt series was used in the publication Cryo-EM structure of the extended type VI secretion system sheath-tube complex (J Wang et. al - Nature microbiology, 2017).
Download tilt series file
An aligned data set can be download from:
wget <not yet available>
This will create a file called ts.mrc in your current working directory.
Inspecting the tilt series
The tilt series at full pixel resolution can be inspected by:
dtmshow
Geometric conventions
In Dynamo, we call stack 3d center to a point (xsc, ysc,zsc ) univocally defined by a stack of micrographs:
- xsc and z and determined by the rotation axis implicitly defined by the alignment.
- y is the center of the stack along direction y, defined as
