Pick Molecules

In cryo-ET, particle picking is a critical step for subsequent subtomogram averaging and structural analysis. Although there are many powerful automatic picking tools available to this field, manual picking is still important for many cases.

In cylindra,

Note

If you want to automatically generate molecules along splines rather than picking one by one, see Spline to Molecules.

Manual pick from tomogram

API: register_molecules

GUI: Molecules > Register molecules

As for drawing splines, manually added points in the napari viewer can be converted into molecules with this method. Regardless of how the points were added, this method will work properly without affecting macro recording, as long as the points are added in the drawing layer. This means that you can use any functionalities or napari plugins to pick molecules.

Manual pick along splines

GUI: Image > Open manual picker

Because cylindra has many functions to manipulate splines, sometimes picking molecules along splines will be more efficient. This is especially useful to look for binding proteins along cylindrical structures, such as MAPs on microtubules.

The manual picker widget in cylidnra is designed for this purpose. It makes a "plane" along the specified spline which can be moved, rotated or shifted relative to the spline. You can imaging you set a camera on a drone and fly it in the spline orbit; you can change the camera angles and focus to take pictures.

The center of the plane is first defined by the specified position on the spline. The plane normal is parallel to the spline tangent vector, so that the plane is always perpendicular to the spline by default. The plane is first rotated by roll, pitch and yaw Euler angles, and focus offset is applied (shifted towards the direction defined by the plane normal vector). Finally, tomogram is sliced by the user defined width and depth.

You can click the 2D slice to add molecules. These molecules are linked to the napari viewer; they are directly added to the napari drawing layer, and all the points in the drawing layer will appear in the 2D slice if it is near the plane.