Volume list file
Volume list files are text files with extension .vll. They are used as an easy interface to describe sets of tomograms and attached models.
Contents
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:
- # Comment
- * 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
- * label = testCatalogue_2
- > Crop particles from this source
- ! 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