The catalogue is a simple way to keep track of the work that has been done on groups of tomograms. This work normally aims at the definition of positions (and possibly orientations) inside each tomogram, so that subvolumes can be defined and cropped, to produce an unique data folder with its corresponding table that can be feed into a project for alignment or classification.
If you have already a set of subtomograms, you have already all the initial orientations you could reasonably extract from the tomograms and you don't want to extract the tomograms again, you probably don't need to define a catalogue. You already have all you need to start designing alignment projects.
Keeping a catalogue is not necessary for cropping particles out of your tomograms. The tools associated with the catalogue can easily be used independently at any stage. We however encourage you to organize your tomograms in a catalogue from the very beginning, as this induces a very smooth workflow and eliminates lengthy administrative overheads that are prone to happen on a later stage.
The best way to get familiar with the logic of the Dynamo catalogues is by generating a test catalogue for a set of automatically created toy tomograms.
In the command line, most functionalities are accessible trough the dcm command. Type help dcm for an exhaustive list.
Note that if you apply these functionalities on a catalogue currently in scope in the dcm gui, the GUI will not update automatically. You need to press explicitly on the [list volumes] button. If these functionalities are invoked through the GUI, however, the list in the GUI will update automatically.
Creating a catalogue
In the command line, you can just type:
dcm -create myCatalogue
It will create a new catalogue in the current folder. It will appear as a folder called myCatalogue and a file called myCatalogue.
Entering a set of tomograms
You can enter directly a set of tomograms in the moment of creation of the catalogue through the flag fromvll
dcm -create myCatalogue -fromvll myList.vll
Here myList.vll is a volume list. This is just a text file; the syntax can be rather complex, but in its simplest form it can be just a file with a tomogram file name at each line, like:
or you can pass metadata of each tomogram
tomogram1.mrc * def=1.2; * apix=0.6; * ftype =1; * ytilt = -45 60; tomogram2.mrc
This metadata can be also passed in a later stage by editing the dcm GUI.
Into an existing catalogue
In this case, the flag is addvll and you use the c flag to select an already exisitng catalogue (instead of create).
dcm -c myCatalogue -addvll myList.vll
Entering a single tomogram
You can use the addTomogram (short at) flag:
dcm -c myCatalogue -at myTomogram.em
to add a single tomogram to an existing catalogue.