Walkthrough on localized reconstruction

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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.

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:

  • x 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