Dipole set models

The dipole set model allows to gather sets of dipoles, each one being an assemble of 3d points called center,north, south and west. Not every point needs to be defined.

When a table is extracted from a dipole set model, each dipole will define a separate particle (i.e., a row in the table). The cropping points will be located each on the center property of each dipole. The cropping angles will be computed so that z direction of the particle is colinear with the north to center axis of the dipole. I a west point is present, the west to center axis will define the x axis of the particle.

The qualified name of the model class in dmodels.dipoleSet.

Applications

Oriented particles

Sometimes it is useful to be able to directly collect the orientation of the particle from a simple interaction with the tomogram (obviously only for particles with a clearly identifiable directionality). For large data sets, it is not advisable to try to click all your particles with this model: the way we normally use it is to collect moderate numbers of particles (in the order of magnitude of the tenths) to construct an initial reference.

Sets of vesicles

Each dipole has four points available, which can be used with full flexibility as geometrical markers. We frequently use the north and the center to mark vesicular entities in a given tomogram (each dipole being a separate vesicle, and using a single dipole set model to encompass all the models). Some manipulation from the command line allows then to create a real vesicle model for ach dipole in the dipole set model.

Edition in dtmslice

Dipole set can be defined on screen in the dtmslice volume browser. When the active model is of type dipole set , a number of keyboard controls are activated. The procedure is to input (some of) the points that define a dipole and then pass to the next one.

The points on the currently dipole appear bigger than in the other dipoles. The current dipole has a green square selection mark, so that you can see it while it is ocluded by other elements in the scene (like the tomogram slice). A dipole that comprises the center and at least other point will be shown inside a transparent enclosing sphere. If this sphere shadows the dipole, you can secondary click on it and then press the option to hide the graphical depiction. When the enclosing sphere is not visible, you can secondary click on the dipole itself to delete it.

Select points in the current dipole

• [c] creates or shifts the center point in the current dipole.
• [n] creates or shifts the norht point in the current dipole.
• [s] creates or shifts the south point in the current dipole.
• [w] creates or shifts the west point in the current dipole.

While you remain in the same dipole, pressing any of this keys will redefine the corresponding point.

Change current dipole

• [<] or [leftarrow] Moves the current dipole one down.
• [n] or [rightarrow] Moves one current dipole one up.
• [enter] opens a new, empty dipole and makes it active.
  • If the dipole with the highest label is empty, it makes it active, instead of creating a new one.
  • It briefly shows a window announcing the label of the created dipole.
• [?] Writes the labels of the dipoles that have been defined.