Difference between revisions of "Walkthrough on membrane models"

From Dynamo
Jump to navigation Jump to search
Line 7: Line 7:
  
 
[[ File:membrane_step_1.png |thumb|center| 700px|]]
 
[[ File:membrane_step_1.png |thumb|center| 700px|]]
 +
 +
A new tomogram entry appears in the catalogue manager. Any further annotations (models) to the tomogram will be linked to this entry. Select the entry and open it:
 +
 
[[ File:membrane_step_2.png |thumb|center| 700px|]]
 
[[ File:membrane_step_2.png |thumb|center| 700px|]]
 +
 +
A tomogram viewer opens. You might need to adjust the contrast (blue arrow). To move through the tomogram slices, you can either use the mouse wheel, click and drag the tomogram slice up and down (orange arrows), or move the position control left and right (orange box).
 +
 
[[ File:membrane_step_3.png |thumb|center| 700px|]]
 
[[ File:membrane_step_3.png |thumb|center| 700px|]]
 +
 +
== Manual annotation ==
 +
 +
The annotation of the membrane surface is done within a so called ''model''. We open a new model of type ''surface'' as follows:
 +
 
[[ File:membrane_step_4.png |thumb|center| 700px|]]
 
[[ File:membrane_step_4.png |thumb|center| 700px|]]
 +
 +
 +
We now add manually add model points along the surface of the membrane. To do that, first move the slice up to a high z height. Then place the mouse cursor on the membrane and press the key [c] on your keyboard. This adds a new model point. Continue adding model points as shown below. Use the right-click to delete points if needed. Note: A known bug may cause the clicked points to be generated slightly displaced from the mouse cursor. Maximize the window of the tomogram viewer to get rid of this effect.
 +
 
[[ File:membrane_step_5.png |thumb|center| 700px|]]
 
[[ File:membrane_step_5.png |thumb|center| 700px|]]
 +
 +
Move the slice down a bit and continue adding points on this new height as shown below:
 +
 
[[ File:membrane_step_6.png |thumb|center| 700px|]]
 
[[ File:membrane_step_6.png |thumb|center| 700px|]]
 +
 +
Repeat this procedure for the full structure until you get something similar to the results shown below:
 +
 
[[ File:membrane_step_7.png |thumb|center| 700px|]]
 
[[ File:membrane_step_7.png |thumb|center| 700px|]]
 +
 +
We now need to define where is the "inside" of the structure. Move the slice somewhere in the middle, place your mouse cursor in the center of the structure and press the key combination of [shift]+[c]:
 +
 
[[ File:membrane_step_8.png |thumb|center| 700px|]]
 
[[ File:membrane_step_8.png |thumb|center| 700px|]]
 
[[ File:membrane_step_9.png |thumb|center| 700px|]]
 
[[ File:membrane_step_9.png |thumb|center| 700px|]]

Revision as of 14:28, 12 August 2021

This walkthrough is a step-by-step guide that teaches how to extract subtomograms from structures with large surfaces (e.g., membranes) using the Dynamo surface models.

Data

We are going to demonstrate the basic ideas and tools on a synthetic dataset. This data is already available in the catalogue manager. It can be accessed by first opening the catalogue manager using the command:

dcm

After the catalogue manager opens, we create the synthetic tomogram that includes a large surface (membrane) in the following way:

Membrane step 1.png

A new tomogram entry appears in the catalogue manager. Any further annotations (models) to the tomogram will be linked to this entry. Select the entry and open it:

Membrane step 2.png

A tomogram viewer opens. You might need to adjust the contrast (blue arrow). To move through the tomogram slices, you can either use the mouse wheel, click and drag the tomogram slice up and down (orange arrows), or move the position control left and right (orange box).

Membrane step 3.png

Manual annotation

The annotation of the membrane surface is done within a so called model. We open a new model of type surface as follows:

Membrane step 4.png


We now add manually add model points along the surface of the membrane. To do that, first move the slice up to a high z height. Then place the mouse cursor on the membrane and press the key [c] on your keyboard. This adds a new model point. Continue adding model points as shown below. Use the right-click to delete points if needed. Note: A known bug may cause the clicked points to be generated slightly displaced from the mouse cursor. Maximize the window of the tomogram viewer to get rid of this effect.

Membrane step 5.png

Move the slice down a bit and continue adding points on this new height as shown below:

Membrane step 6.png

Repeat this procedure for the full structure until you get something similar to the results shown below:

Membrane step 7.png

We now need to define where is the "inside" of the structure. Move the slice somewhere in the middle, place your mouse cursor in the center of the structure and press the key combination of [shift]+[c]:

Membrane step 8.png
Membrane step 9.png
Membrane step 10.png
Membrane step 11.png
Membrane step 12.png
Membrane step 13.png
Membrane step 14.png
Membrane step 16.png
Membrane step 17.png
Membrane step 18.png
Membrane step 19.png
Membrane step 20.png
Membrane step 21.png
Membrane step 22.png
Membrane step 23.png