Difference between revisions of "Advanced starters guide"
| Line 21: | Line 21: | ||
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: | + | This should have created the file called <tt>crop.rec</tt> in your current directory. |
| + | |||
| + | ===Size check of a file=== | ||
| + | |||
| + | 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> | ||
| Line 29: | Line 33: | ||
<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. | ||
| + | ===Lightweight visualization=== | ||
| + | We can inspect quickly its contents with | ||
| + | |||
| + | <tt>dtmshow -otf crop.rec</tt> | ||
| + | |||
| + | 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. | ||
| + | |||
| + | |||
| + | [[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.
Contents
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.
