Catalogue

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 main tool to work with catalogues is the dcm GUI, that also provides command line functionality to create, edit an extract information from catalogues. Help on command syntax: dcm

Getting started

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.

If you already have a data set of several tilt series, you can check our general guidelines for organization of tomography projects. These guidelines sketch a comfortable way to organize your raw data and create your first catalogue.

Basic functionalities

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

During creation

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:

tomogram1.mrc 
tomogram2.mrc

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.