The Atom Selection Editor

The Atom Selection Editor, reached via the Tools=>Atom Selection menu path, specifies selection capabilities and tool preferences. It is illustrated below:

ed_selection.tif
The Atom Selection Editor
In this example, we are preparing to expand the selection to atoms bonded to already-selected atoms.

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The buttons at the top of the dialog provide ways to select all atoms, no atoms, or the atoms within a specific atom group. The latter two buttons function as pull-down menus whose contents consist of all defined atom groups for the current structure (as in the example above where two different group classes are defined).

The checkboxes and popup menu in the central portion of the dialog specify defaults for the two selection modes. They have the following meanings:

Item Meaning
Mouse Selection in View Specifies the default selection mode in View windows:
Allow Click Deselection When unchecked, clicking again on a selected atom has no effect.
Additive Rubberband Selection When unchecked, each marquee selection replaces the current selection rather than adding to it.
Allow Rubberband Deselection When checked, a marquee selection toggles the select status of all atoms in the enclosed region.
Allow Brush Deselection When checked, a brush selection operation toggles the select status of all touched atoms.
Clear Selections After Use When unchecked, selections are retained even after an operation has acted on the component atoms.

The Expand Selection slider allows you to expand a selection to include atoms adjacent to already selected ones. The Using popup specifies how “adjacent” atoms are identified: by bonding, by absolute distance regardless of bonding, or by PDB residue. The choice made here affects what atoms will be added to the selection as the slider is moved to the right, and the Up To field indicates the maximum value corresponding to the right end of the slider: number of bonds, distance in Angstroms, or number of residues. Thus, moving the slider all the way to the right when Up To is 5 and Bond is selected will select all atoms within 5 bonds of all currently selected atoms. When PDB Residue is selected, then each step selects an entire PDB residue.

The list of selected atoms appears in the final Atoms field, which you can also edit directly.