Difference between revisions of "Advanced starters guide"

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unter MacOS.
 
unter MacOS.
  
This should have created the file called <tt>crop.rec</tt> in your current directory. You're probably curious to see what's inside, so that let's write first:
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This should have created the file called <tt>crop.rec</tt> in your current directory.  
 +
 
 +
===Size check of a file===
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 +
You're probably curious to see what's inside, so that let's write first:
  
 
  <tt>dfile crop.rec</tt>
 
  <tt>dfile crop.rec</tt>
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   <nowiki>filetype: volume
 
   <nowiki>filetype: volume
 
  size: 1285 x 956 x 786</nowiki>
 
  size: 1285 x 956 x 786</nowiki>
 +
 +
So, it's a tomogram.
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===Lightweight visualization===
 +
We can inspect quickly its contents with
 +
 +
<tt>dtmshow -otf crop.rec</tt>
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 +
Hereby, the flag <tt>-otf</tt> means "on the fly", telling <tt>dtmshow</tt> to ''not'' preload the full tomogram, but to access in disk the individual slices that are needed when inspecting a particular area.
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 +
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[[File:FhvTomoshowOnTheFly.png|thumb|center|500px|Basic controls of <tt>dtmshow</tt>]]

Revision as of 19:13, 15 July 2017

This walkthrough uses a small size example based on a real tomogram to covers several tasks.


The example data set

The data is a fraction of a tomogram. The full tomogram was used in "Cryo-electron tomography reveals novel features of a viral RNA replication compartment." (Ertel et al.), and represents several FHV viruses docked in the membrane of a mythocondrion.


Downloading

In principle, you can download all the files related to this example with the command:

 dpkhelp.wiki.downloadExample('fhv');

If it fails under Matlab or the Dynamo command line, you can try to directly use the linux order

wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/crop.rec 

or

curl -O  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/crop.rec 

unter MacOS.

This should have created the file called crop.rec in your current directory.

Size check of a file

You're probably curious to see what's inside, so that let's write first:

dfile crop.rec

to let Dynamo check the dimensions of the file. The header of a .rec file is readed as a regular mrc, yielding:

 filetype: volume
 size: 1285 x 956 x 786

So, it's a tomogram.

Lightweight visualization

We can inspect quickly its contents with

dtmshow -otf crop.rec

Hereby, the flag -otf means "on the fly", telling dtmshow to not preload the full tomogram, but to access in disk the individual slices that are needed when inspecting a particular area.


Basic controls of dtmshow