Difference between revisions of "Walkthrough for lattices on vesicles"

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(Created page with "This walkthrough shows the approach to process proteins that cover spheroidal vesicles following (approximately) a structured lattice. For demonstration, we use a highly binne...")
 
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We are interested in cropping the particles between the two layers of each one of the viruses.
 
We are interested in cropping the particles between the two layers of each one of the viruses.
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In our approach, we will first use a single model to manually input the approximate centers and radiuses of all the viruses. We will use the model type <tt>dipoleSet</tt>. This model allows to describe each annotated virus as a ''dipole'': we will mark the (approximate) center of the virus as the <tt>center</tt> property of a dipole. The radius of the virus will be described by an annotation of the <tt>north</tt> property of the dipole. 
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[[File:HivSelectModel.png|thumb|center|600px| Selecting the ''dipoleSet'' model ]]
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When the model is active, we use the key <tt>c</tt> to mark the <tt>center</tt> of the current dipole, and <tt>n</tt> to mark the north.
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[[|thumb|center|600px| Selecting a ''dipole'': click on <tt>C</tt> for the center, then <tt>N</tt> for the north]]
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Further clicks on <tt>c</tt> or <tt>n</tt> will just move the

Revision as of 15:44, 26 July 2017

This walkthrough shows the approach to process proteins that cover spheroidal vesicles following (approximately) a structured lattice. For demonstration, we use a highly binned tomogram with several viral capsides.

Data

The data has been made available by Florian Schur . This single tomogram is part of the data set used for the paper:


Getting the data

You can download the data through:

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Viewing the data

The tomogram is severely binned, so it will probably fit in memory without major problems. We can just use our typical tool to quick check a tomogram.

 dtmshow v17.rec 


Particle cropping

We are interested in cropping the particles between the two layers of each one of the viruses.

In our approach, we will first use a single model to manually input the approximate centers and radiuses of all the viruses. We will use the model type dipoleSet. This model allows to describe each annotated virus as a dipole: we will mark the (approximate) center of the virus as the center property of a dipole. The radius of the virus will be described by an annotation of the north property of the dipole.

Selecting the dipoleSet model

When the model is active, we use the key c to mark the center of the current dipole, and n to mark the north.

[[|thumb|center|600px| Selecting a dipole: click on C for the center, then N for the north]]

Further clicks on c or n will just move the