All About Selections: From Atoms to Fragments, Residues, Chains, and Beyond

GaussView has a wide variety of different methods and techniques for selecting atoms within molecular structures. Groups of selected atoms are used for many purposes in building structures and setting up Gaussian jobs. This section will discuss the various alternatives, which are summarized in the following list:

Selection-Related Toolbar Icons

i_pick_click.tif i_pick_marquee.tif w_picked.tif
The main window builder toolbar and the standalone Builder palette both contain icons that control item-selection behavior and place the cursor in a dedicated selection mode. The icon on the left sets the selection mode to clicking: clicking on an atom toggles its selection mode. Selected atoms appear light yellow (see the two leftmost atoms in the illustration at the right above), and their serial numbers are displayed. Contrast this to highlighting, where atoms are displayed in light blue for easy identification and/or location (e.g., the hydrogen atom at the lower right). If an atom is both selected and highlighted, it appears light blue (highlighted).

The second selection mode is marquee mode, also called rubberband mode (the second icon from the leftt at the head of this section). In this mode, pressing and holding the mouse button while dragging the cursor will draw a rectangle in the view. When the mouse button is released, all atoms within the defined area are added to the selection.

The final selection mode is brush mode. In this mode, dragging the mouse selects all atoms that fall under the cursor.

Variations to the default functioning for all modes are available via the Atom Selection dialog discussed below.

i_select_all.tif i_select_none.tif
The other two selection-related icons are the Select All and Select None buttons, which select and deselect all atoms in the molecule, respectively.

Selection Keystrokes in View Windows

These same selection options are available at all times in any View window via the following keystrokes (which are not case-sensitive), regardless of the current toolbar icon selection:

Key Effect
a Select all atoms.
n Deselect all atoms (select no atoms).
r Marquee selection is active while the R key is held down.
c Individual atom click mode selection is active while the C key is held down.
b Brush selection mode is active while the B key is held down.

Selecting with the Atom List Editor and Similar Tools

The Atom List Editor provides a spreadsheet-like mechanism for viewing and modifying molecular structures and parameters. The same facilities are also provided by the PDB Residue Editor and PDB Secondary Structure Editor.


The Atom List Editor

There are three main selection-related features in these dialogs:

Selection functionality is also present in the Group Actions menu of the Atom Group Editor:


The Atom Group Editor
The final items on the Group Actions menu select/deselect the atoms in the current atom group (here, fragment 2).

The Atom Selection Editor

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

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The Atom Selection Editor

This dialog allows you to select all atoms, no atoms, and to select and deselect by atom group. It also sets default behaviors for the various selection modes. You can also expand the current selection to adjacent atoms using the slider, with proximity defined by bonding, distance, or PDB residue, as well as a maximum value. Detailed information about it is available here.