Difference between revisions of "Video tutorials"

From Dynamo
Jump to navigation Jump to search
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
== Starting Guide ==
 
== Starting Guide ==
  
This [[youtube https://youtu.be/SWKyHrLETPQ]] shows an introduction to setting up alignment projects in ''Dynamo''.
+
This [[https://youtu.be/SWKyHrLETPQ youtube link]] shows an introduction to setting up alignment projects in ''Dynamo''. It works on the old {{t|dynamo_project_manager}} GUI.
  
 
==Particle picking ==
 
==Particle picking ==
Line 10: Line 10:
  
 
==== Isolated particles ====
 
==== Isolated particles ====
We use {{t|dtmview}} to show how the concurrent viewers can be used to pick isolated particles.
+
 
 +
In this [https://youtu.be/VPIdxpxNqWw video] we use {{t|dtmview}} to show how the concurrent viewers can be used to pick isolated particles.
 
The tomogram represents a mixture of PRD1 bacteriophages in a buffer.
 
The tomogram represents a mixture of PRD1 bacteriophages in a buffer.
 +
 +
Tomogram is courtesy of the Abrescia Lab, in CIC-Biogune (Bilbao).
  
 
==== Arbitrary membranes ====
 
==== Arbitrary membranes ====
We use {{t|dtmslice}} and the {{t|montage viewer}} to define points in a membrane in a semiautomatic manner.
+
In [https://youtu.be/2V1pD0Gr8L8 this video] we use {{t|dtmslice}} and the {{t|montage viewer}} to define points in a membrane in a semiautomatic manner.
 +
Tomogram is courtesy of Morgan Beeby, in Imperial College (London).
  
 
==== Filaments ====
 
==== Filaments ====
{{t|dtmslice}} is used to pick microtubules in a tomogram.
+
In [https://youtu.be/hsZ-9xAYufIt this video], {{t|dtmslice}} is used to pick microtubules in a tomogram. We use {{t|dpreview}} to inspect the tomogram and select an area that is then read into memory.
 +
This region is then displayed in {{t|dtmslice}}. With keys [1] and [2] we can define extremal points of a filament, ask Dynamo to define local views that are orthogonal to the path between points [1] and [2]. In these local views the user can click on the center of each section of the filament, defining a coarse approximation to the path. 
 +
The tomogram is courtesy of Takashi Ishikawa, in PSI-Villingen (Switzerland).

Latest revision as of 09:24, 1 June 2016

Starting Guide

This [youtube link] shows an introduction to setting up alignment projects in Dynamo. It works on the old dynamo_project_manager GUI.

Particle picking

Catalogues

Models

Isolated particles

In this video we use dtmview to show how the concurrent viewers can be used to pick isolated particles. The tomogram represents a mixture of PRD1 bacteriophages in a buffer.

Tomogram is courtesy of the Abrescia Lab, in CIC-Biogune (Bilbao).

Arbitrary membranes

In this video we use dtmslice and the montage viewer to define points in a membrane in a semiautomatic manner. Tomogram is courtesy of Morgan Beeby, in Imperial College (London).

Filaments

In this video, dtmslice is used to pick microtubules in a tomogram. We use dpreview to inspect the tomogram and select an area that is then read into memory. This region is then displayed in dtmslice. With keys [1] and [2] we can define extremal points of a filament, ask Dynamo to define local views that are orthogonal to the path between points [1] and [2]. In these local views the user can click on the center of each section of the filament, defining a coarse approximation to the path. The tomogram is courtesy of Takashi Ishikawa, in PSI-Villingen (Switzerland).