Difference between revisions of "Walkthrough on filament models"

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This walkthrough is a step-by-step guide that teaches how to extract subtomograms along filament-like structures using the ''Dynamo'' filament models.
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This walkthrough is a step-by-step guide that teaches how to extract subtomograms from filament-like structures using the ''Dynamo'' filament models.
  
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==Data ==
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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:
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<tt>dcm</tt>
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After the catalogue manager opens, we create the synthetic tomogram that includes tubular looking objects in the following way:
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[[ File:filament_step_1.png |thumb|center| 600px|step]]
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The catalogue manager will create a catalogue to archive the created tomogram and also the models that we will create around it.
  
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
 
  
  
>> dcm
 
to start the catalogue manager:
 
  
  
  
== Data ==
 
We prepared a set of 6 tomograms, each containing one Immature HIV-1 virus like particle (VLP) with a layer formed by a lattice of capsid proteins. The capsid proteins have a C6 symmetry, a diameter of roughly 15nm and a molecular weight of about 150kDa. The pixelsize of the tomograms is 2.7 angstrom. You can find the tomograms in:
 
<tt>~/data/tutorial_VLPs</tt>
 
 
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Revision as of 15:36, 10 August 2021

This walkthrough is a step-by-step guide that teaches how to extract subtomograms from filament-like structures using the Dynamo filament 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 tubular looking objects in the following way:


step


The catalogue manager will create a catalogue to archive the created tomogram and also the models that we will create around it.




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