Difference between revisions of "Walkthrough for lattices on vesicles"

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(Getting the data)
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[[ HivDtmshow.png |thumb|center|500px| <tt>dtmshow</tt> on the sample tomogram. ]]
 
[[ HivDtmshow.png |thumb|center|500px| <tt>dtmshow</tt> on the sample tomogram. ]]
  
== Particle cropping ==
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== Annotation of a tomogram ==
  
 
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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Here, the user probably clicked on <tt>c</tt> for vesicle 2 in its real center, then clicked on <tt>n</tt> for the north point, and then moved to vesicle 3, clicking on <tt>c</tt> trying to mark the center. As a new dipole  was not opened (i.e., the <tt>enter</tt> key was not pressed) when the vesicle 2 was finished, the center of vesicle 2 got misplaced.  When this happens, simply press on <tt>h</tt> to hide the spheres and click the center of vesicle 2 back in its position. Then, press on <tt>enter</tt> to start the next vesicle.
 
Here, the user probably clicked on <tt>c</tt> for vesicle 2 in its real center, then clicked on <tt>n</tt> for the north point, and then moved to vesicle 3, clicking on <tt>c</tt> trying to mark the center. As a new dipole  was not opened (i.e., the <tt>enter</tt> key was not pressed) when the vesicle 2 was finished, the center of vesicle 2 got misplaced.  When this happens, simply press on <tt>h</tt> to hide the spheres and click the center of vesicle 2 back in its position. Then, press on <tt>enter</tt> to start the next vesicle.
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 +
When you are finished, don't forget to save the tomogram into the catalogue
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 +
== Cropping the particles ==
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 +
We will describe a protocol to be carried from the command line, explaining each step. In short, we will visit each dipole in the model we just created, define a spherical vesicle centered on the dipole, use it to define a regular distribution of points on each vesicle, define positions pointing outwards and format everything as a [[table]] that can be used directly by ''Dynamo'' to operate an extraction and a subsequent alignment.
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=== Extracting information from the catalogue ===
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 +
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=== Create a table for each vesicle ===
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==== Merging the tables ===
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=== Create a data folder ===
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=== Create an average ===
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=== Recroping the particles ==
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<tt>help dmodels.dipoleSet.getTableFromEnclosingSpheres</tt>

Revision as of 17:03, 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 the command:

dpkhelp.wiki.downloadExample('hiv');

In case this command files, please try the direct link:

wget to be filled XXX

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 

thumb|center|500px| dtmshow on the sample tomogram.

Annotation of a tomogram

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


Structure to average


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. It will create a semitransparent sphere enclosing the completed dipole.

Selecting a dipole: click on C for the center, then N for the north

Further clicks on c or n will just move the center or the north of the same dipole. In order to click a further dipole, you need to click on enter and "open" the next dipole for clicking. If you forget to click on enter before annotating points on the next vesicle, you'll end up with situation like this:

Wrong input: enter needed to be clicked between vesicles 2 and 3

Here, the user probably clicked on c for vesicle 2 in its real center, then clicked on n for the north point, and then moved to vesicle 3, clicking on c trying to mark the center. As a new dipole was not opened (i.e., the enter key was not pressed) when the vesicle 2 was finished, the center of vesicle 2 got misplaced. When this happens, simply press on h to hide the spheres and click the center of vesicle 2 back in its position. Then, press on enter to start the next vesicle.

When you are finished, don't forget to save the tomogram into the catalogue

Cropping the particles

We will describe a protocol to be carried from the command line, explaining each step. In short, we will visit each dipole in the model we just created, define a spherical vesicle centered on the dipole, use it to define a regular distribution of points on each vesicle, define positions pointing outwards and format everything as a table that can be used directly by Dynamo to operate an extraction and a subsequent alignment.

Extracting information from the catalogue

Create a table for each vesicle

= Merging the tables

Create a data folder

Create an average

= Recroping the particles

help dmodels.dipoleSet.getTableFromEnclosingSpheres