# Subboxing

Subboxing is the technique of locating the position of subunits inside *data* particles.
When an average is available, is possible to express the positions of the subunits of interest with relation to the center of the average. Then, the alignment table that produced the average can be used to produce a *subboxed table* that locates the subunits in the data. This subboxed table can be used to recrop a new data folder, in which each particle file will contain a subunit.

## Contents

## Orientation of subboxed particles

Each subboxed particle file will contain a subunit. The density map particle itself is stored (as always in *Dynamo*) without any rotation: the fact the different subunits will (possibly) have different orientations will always be expressed through the metadata, that is, it will be reflected in the subboxed table.

## Creation of subboxed tables

The fundamental command is `dsubboxing_table`

subboxedTable = dynamo_subboxing_table(table,centeredPoint);

Here, the `centeredPoint` point is expressed in relation to the center point of the average.

## Symmetry subboxing

Subboxing is frequently used to extract several symmetrically related subunits out of each particle. The general syntax for this case is:

subboxedTable = dynamo_subboxing_table(table,centeredPoint,'sym',symmetryOperator);

There are different values that can be used as symmetry operator: `'Cn'`, `'Dn'`,`'ico'`,`'ico_vertex'`. The position of the symmetry axes is fixed by convention on each case.

### Cn symmetry

The symmetry axis goes along the direction *z* and passes through the center of the volume

### Icosahedral symmetry

#### Pentons

Pentons are centered on the C5 symmetry axes of the particle. As the orientation is defined by the convention, it is only necessary to provide the distance of a reference penton to the center.

The 12 orientations can be computed as:

pentonNormals = dpkgeom.symmetry.ico.directionsC5Axises();

Then, the location of a penton situated `r` pixels away is simply given by

locationPenton = r*pentonNormals(1,:);

for position 1 (arbitrarily chosen). Then, the subboxed table can be computed:

subboxedTable = dynamo_subboxing_table(table, locationPenton,'sym','ico_vertex');

### Custom symmetry

It is possible to pass a text file containing all symmetry operators, expressed as matrices.