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:
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.
The other two selection-related icons are the and buttons, which
select and deselect all atoms in the molecule, respectively.
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. |
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 Atom Group Editor:
menu of the
The Atom Group Editor
The final items on the menu
select/deselect the atoms in the current atom group (here, fragment 2).
The Atom Selection Editor, reached via the menu path, brings selection capabilities and tool preferences. It is illustrated below:
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.