Volume list file

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Volume list files are text files with extension .vll. They are used as an easy interface to describe sets of tomograms and attached models.

Syntax

A volume list file just lists tomogram files, letting the user attach under each line representing a tomogram some information about it. A comment is represented by a # symbol. A text file as:

myTomogram1.mrc
myTomogram2.mrc
myTomogram3.mrc
# tomogram 4 was awful!, we exclude it!
myTomogram5.mrc

is already a perfectly formatted volume list file that can be used for instance to create a catalogue

Advanced syntax

Depending on the final use of the volumen file (possibly creating a catalogue from anew or cropping particles), there are several special characters that introduce different operations:

  1. # Comment
  2. * Parameter assignation (ftype,ytilt, etc)
    * label = testCatalogue_2
    • index = 2
    * ftype = 1
    * xtilt = -60 60
    * ytilt = -60 60
    * ztilt = -60 60
    * apix = 1.20
    * defocus = 2.40
  3. > Crop particles from this source
  4. ! Import models from this source

Cropping particles

= Manually

Volume list files are useful to extract particles from multiple tomograms into the same data folder. This can be achieved from the command line with the order:

dtcrop <vll file> reorder sidelength datafolder

so, a command in real life would look like: dtcrop mylist.vll reorder 64 data;

Here, myList.vll is a file text that lists tomogram files. Below each tomogram, one can insert one or several files models or tables preceded with the symbol >

myTomogram1.mrc
> myTable1.tbl
myTomogram2.mrc
> myTable2.tbl
> myModel_imported.omd
# we can mix models an tables
myTomogram5.mrc
# a volume may have no sources


Through the catalogue

Creating catalogues