The Atom Selection Editor
The Atom Selection Editor, reached via the menu path, specifies selection capabilities and tool preferences. It is illustrated below:
The Atom Selection Editor
In this example, we are preparing to expand the
selection to atoms bonded to already-selected atoms.
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 |
Specifies the default selection mode in View
windows:![]() |
|
When unchecked, clicking again on a selected atom has no effect. | |
When unchecked, each marquee selection replaces the current selection rather than adding to it. | |
When checked, a marquee selection toggles the select status of all atoms in the enclosed region. | |
When checked, a brush selection operation toggles the select status of all touched atoms. | |
When unchecked, selections are retained even after an operation has acted on the component atoms. |
The
slider allows you to expand a selection to include atoms adjacent to already selected ones. The 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 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 is 5 and is selected will select all atoms within 5 bonds of all currently selected atoms. When is selected, then each step selects an entire PDB residue.The list of selected atoms appears in the final
field, which you can also edit directly.