Difference between revisions of "Walkthrough on localized reconstruction"
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* create a reconstruction at low resolution | * create a reconstruction at low resolution | ||
* mark the coordinates of interest in the low resolution reconstruction | * mark the coordinates of interest in the low resolution reconstruction | ||
| − | * reconstruct separately the different coordinates. | + | * reconstruct separately the different coordinates at full resolution |
| + | |||
| + | For the sake of simplicity, in this walkthrough, the landmarks of interest will be simply the gold beads, which are trivially recognizable both in tomograms and in projections in the tilt series. | ||
== Example data set == | == Example data set == | ||
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* ''x<sub>sc</sub>'' and ''z<sub>sc</sub>'' and determined by the rotation axis implicitly defined by the alignment. | * ''x<sub>sc</sub>'' and ''z<sub>sc</sub>'' and determined by the rotation axis implicitly defined by the alignment. | ||
* ''y<sub>sc</sub>'' is the center of the stack along direction ''y'', defined as <tt>floor(Ny/2)+0.5;</tt> for a tilt series with Ny pixels along ''y''. | * ''y<sub>sc</sub>'' is the center of the stack along direction ''y'', defined as <tt>floor(Ny/2)+0.5;</tt> for a tilt series with Ny pixels along ''y''. | ||
| + | |||
| + | == Creation of a binned reconstruction == | ||
| + | |||
| + | === Binned tilt series === | ||
| + | |||
| + | === Filtered tilt series === | ||
| + | |||
| + | === Reconstruction === | ||
| + | |||
| + | == Annotation on binned reconstruction == | ||
Revision as of 17:36, 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 at full resolution
For the sake of simplicity, in this walkthrough, the landmarks of interest will be simply the gold beads, which are trivially recognizable both in tomograms and in projections in the tilt series.
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 zsc and determined by the rotation axis implicitly defined by the alignment.
- ysc is the center of the stack along direction y, defined as floor(Ny/2)+0.5; for a tilt series with Ny pixels along y.
