Walkthrough on localized reconstruction

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.

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 (x_sc, y_sc,z_sc) univocally defined by a stack of micrographs:

• x_sc and z_sc and determined by the rotation axis implicitly defined by the alignment.
• y_sc 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.