Proximity Dialog Box

The Proximity dialog box provides tools to select atoms based on their distance from the atoms defined by the current selection (the source atoms).

To open this dialog box, click the Proximity button in the Atom Selection Dialog Box.

Using
Features
Additional Resources

Using the Proximity Dialog Box

In the Proximity dialog box, you can select atoms that are within a certain distance of the source atoms, or atoms that are beyond a certain distance from the source atoms. You can also choose to restrict the selection to only the atoms that are within or beyond the prescribed distance, or to include atoms that belong to the same molecule or residue - "filling" in the molecule or residue. If you fill molecules or residues within the chosen distance, some atoms will lie beyond that distance; likewise if you fill beyond the chosen distance, some atoms will lie within that distance.You can also include or exclude the source atoms from the selection.

Proximity section

The Proximity section provides options for the region to select atoms from and the units of distance for the boundary, and a text box to specify the distance value.

Within: Atoms within the boundary are selected.
Beyond: Atoms beyond the boundary are selected.
Angstroms: The boundary is defined as a distance in angstroms from the selection. Enter the distance in the text box.
Bonds: The boundary is defined as a distance in terms of the number of bonds from the selection. Enter the number of bonds in the text box.

Fill section

The fill section contains three mutually exclusive options for filling molecules, and a fourth option for handling the source atoms.

None: Only the atoms that lie within or beyond the boundary are included in the selection. No filling is done.
Residues: Atoms in residues that cross the boundary are included in the selection.
Molecules: Atoms in molecules that cross the boundary are included in the selection.
Exclude source: By default, the source atoms are included in the selection. If you want the source atoms excluded, select this option.

Update Markers

This button updates the markers in the Workspace so you can view the selection before clicking OK.