Table of Icons and Menu Items

The following table lists the available icons and menu items along with their functions. Most items will be described in more detail in future sections of this book. Note that on Mac OS X systems, the Equivalent Key modifier is the Command key, not the Control key.

Icon	Name	Menu Path	Purpose	Keystroke
	New	File=>New	Create a new molecule (per submenu selection).
		File=>New=> Create Mol. Group	Create a new (one-member) molecule group as an empty View window.	Ctrl-N
		File=>New=> Add to Mol. Group	Add a new molecule to the current molecule group.	Ctrl-Shift-N
	Open	File=>Open	Open files supported by GaussView.	Ctrl-O
		File=>Recent Files	List of recently-opened files for easy reaccess.
		File=>Related Files	List of files related to the current molecule (e.g., input file, log file, checkpoint file, etc.)
		File=>Refresh	Reload current file in active View window.
	Save	File=>Save	Save molecule(s) in the active molecule group to file(s).	Ctrl-S
		File=>Save	Save any temporary files associated with Gaussian Quick Launch jobs.
	Print	File=>Print	Print the contents of the active View window.	Ctrl-P
	Save Image	File=>Save Image File	Produce a graphics file of current View window.
	Save Movie	File=>Save Movie	Save movie file, movie frame files, or both (selected via submenu).
	Preferences	File=>Preferences	Specify defaults for aspects of GaussView’s behavior.
		File=>Exit	Close all GaussView windows and exit application.
	Undo	Edit=>Undo	Reverse the previous editing action and maintain a list of all previous actions for potential Redo.	Ctrl-Z
	Redo	Edit=>Redo	Reverse the previous Undo operation.	Ctrl-Y
	Cut	Edit=>Cut	Cut the current selection to clipboard.	Ctrl-X
	Copy	Edit=>Copy	Copy the current selection to clipboard.	Ctrl-C
	Paste	Edit=>Paste	Copy clipboard contents to the current model (per submenu selection).
		Edit=>Paste=>Add to Molecule Group	Add the molecule on the clipboard as a new model within the current model group.	Ctrl-V
		Edit=>Paste=> Replace Molecule	Replace current molecule with clipboard contents.
		Edit=>Paste=> Append Molecule	Add molecule on the clipboard to the current model as a separate fragment
	Delete	Edit=>Delete	Remove the current selection.	Ctrl-Shift-V Del
		Edit=>Image Capture	Copy the contents of the active View window to the clipboard.	Ctrl-I
	Atom List Editor	Edit=>Atom List	Edit the molecule’s numerical coordinates and parameters in a spreadsheet-like dialog.
	Redundant Coord. Editor	Edit=>Redundant Coordinates	Specify redundant internal coordinates for the Gaussian ModRedundant option.
	Connection Editor	Edit=> Connection	Specify corresponding atoms in two related molecular structures (e.g., for Opt=QST2 or QST3 input).
	Select Layer	Edit=>Select Layer	Assign atoms to layers graphically for ONIOM calculations.
		Edit=>Atom Groups	Open the Atom Group Editor, useful for defining fragments, ONIOM layers, frozen atoms and other atom groupings.
		Edit=>Atom Selection	Open the Atom Selection Editor, enabling you to perform advanced selection operations.
		Edit=>PDB Residues	Open the PDB Residue Editor which enables operations based on residues as defined in the originating PDB file.
		Edit=>PDB Secondary Structures	Open the PDB Secondary Structure Editor which enables operations based on PDB file secondary structures (e.g., chains and helixes).
		Edit=> Point Group	Specify/impose symmetry on the current model.
	Crystal Editor	Edit=>PBC	Create and modify unit cells for periodic structures.
	MO Editor	Edit=>MOs	View, reorder and modify occupancy for molecular orbitals.
	Symmetrize	Edit=>Symmetrize	Apply point group symmetry to the current model.
		Edit=>Reorient	Restore canonical molecule orientation.
	Rebond	Edit=>Rebond	Recompute the bound atoms, identifying bonded atoms based on a distance algorithm.
	Clean	Edit=>Clean	Adjust molecular geometry according to a set of rules designed to match chemical intuition.
		Edit=>Mirror Invert	Invert the molecule around the selected atom.
	Add View	View=>Add View	Create a new View window, with an independently adjustable view of the current molecule.
	Center	View=>Center	Center molecule in the View window (adjusts size).
		View=>Builder	Close or reopen the standalone Builder palette.
		View=>Hydrogens	Control the display of hydrogens in View window.
		View=>Dummies	Control the display of dummy atoms in View window.
		View=>Labels	If selected, label each atom with its serial number (reflecting its sequence in the list of atoms).
		View=>Symbols	If selected, display the chemical symbol for each atom.
		View=>Bonds	Control the display of bonds in the View window.
		View=>Synchronize	Link views to synchronize mouse-based manipulations.
		View=> Cartesian Axes	Control the display of X,Y,Z axes in the View window.
		View=> Stereochemistry	Indicate molecule’s stereochemistry by labeling relevant atoms as R or S.
		View=>Positioning Tools	Display the molecule positioning tools icons in the View window toolbar.
	Display Format	View=> Display Format	Specify the display format for molecules and surfaces.	Ctrl-D
	Calculation	Calculate=> Gaussian Calculation Setup	Set up Gaussian input for the molecular structure in the current view winodw and optionally run the job.	Ctrl-G
	Quick Launch	Calculate=> Gauss. Quick Launch	Run a Gaussian job for the current molecule, bypassing the Gaussian Calculation Setup dialog.
	Schemes	Calculate=> Gauss. Calc. Scheme	Define and modify Gaussian calculation schemes.
	Current Jobs	Calculate=> Current Jobs	Display currently running GaussView-initiated Gaussian jobs (including CubeGen and FreqChk).	Ctrl-J
		Results=> Summary	Provide summary data of the results of a Gaussian calculation (after a results file is opened).
		Results=>Charge Distribution	Display partial charge density, as computed by various Gaussian methods.
		Results=> Surfaces/Contours	Create, load, save and display surfaces and contours.
		Results=> Vibrations	Display calculated vibrational and other spectral data, including normal mode animation.
		Results=>NMR	Display calculated NMR spectra.
		Results=>UV-VIS	Display predicted UV/Visible spectra.
		Results=>Scan	Display plots of potential energy surface scans.
		Results=>IRC/Path	Display plots of predicted IRC paths.
		Results=>Trajectory	Display trajectory plots from ADMP or BOMD calculations.
		Results=> Optimization	Display plots of geometry optimization results.
	View File	Results=>View File	Start an editor session for the log file for the current molecule.
	Stream	Results=>Stream Output File	Display output from a currently running Gaussian calculation continuously as it becomes available.
		Windows=>Molecule Groups=>Show All	Display/restore windows for all model groups.
		Windows=>Molecule Groups=>Show None	Hide windows for all model groups.
		Windows=>Molecule Groups=>name	Display/restore windows for the specified model group
		Windows=> Minimize All	Minimize all view windows.
		Windows=> Restore	Raise active View window.
		Windows=> Restore All	Open all minimized view windows.
		Windows=>Close	Close the active View window.
		Windows=> Close All	Close all open view windows.
	Previous	Windows=>Previous	Activate the previous View window in sequence.	PgUp
	Next	Windows=>Next	Activate the next View window in sequence.	PgDown
	Cascade	Windows=>Cascade	Arrange all view windows in an overlapped pile.
	Tile	Windows=>Tile	Resize and rearrange view windows so that all are visible.
		Windows=>name	Make the specified View window the active one.
	Help	Help=> GaussView Help	Open the GaussView help facility.	Ctrl-H
		Help=> Gaussian Help	Open the Gaussian website’s help section in the default browser. If Internet access is not available, a local copy included within the GaussView application tree is opened instead.
		Help=> About GaussView	Display the GaussView copyright and version information.
		Help=> GaussView Tips	Display GaussView tips.
	Elements		Open the Element Fragments palette.
	Rings		Access a palette of ring structures.
	R-Group Fragment		Summon a palette of functional group fragments.
	Biological Fragments		Summon a palette of amino acid and nucleoside fragments.
	Custom Fragment		Access a custom fragment library.
	Modify Bond		Access Bond SmartSlide dialog after two atoms are selected.
	Modify Angle		Access Angle SmartSlide dialog after three atoms are selected.
	Modify Dihedral		Access Dihedral SmartSlide dialog after four atoms are selected.
	Inquire		Examine structural data for the current molecule.
	Add Valence		Add an additional hydrogen to the selected atom.
	Delete Atom		Eliminate atoms and/or open valences (dangling half bonds).
	Invert About Atom		Invert molecular structure about a selected atom.
	Select by Clicking		Select atoms by clicking on them.
	Select by Marquee		Select atoms by clicking and dragging a marquee enclosing them.
	Select None		Deselect all currently selected atoms.
	Select All		Select all atoms.
Fragment Placement			Open panel containing fragment placement options within the control window.
Icons found in the Active Model View window:
	Animate		Display all models within the molecule group in succession.
	Stop Animation		Stop an animated display.
	Single View		Display only one model within the molecule group.
	Multi View		Display all models within the molecule group.
Icons found in the five Fragment Palette windows:
	Tacked		Keep this palette open until explicitly closed (amodal operation).
	Untacked		Close palette when a different one is opened (modal operation).
Icons related to various coordinate editing dialogs:
	Z-matrix Coordinates		Display Z-matrix coordinates.
	Cartesian Coordinates		Display Cartesian coordinates.
	Fractional Coordinates		Display fractional coordinates for periodic systems.
	ONIOM Layers		Display ONIOM layer assignments and related data.
	MM Parameters		Display Molecular Mechanics atoms types and other data.
	PDB Info		Display residue and chain assignments from a PDB file.
	Isotope Masses		Display column(s) containing isotopes mass(es).
	Create a New Coordinate		Add a new redundant coordinate in the Redundant Coordinate Editor.
	Sort Ascending		Sort rows in ascending order in the Atom List Editor.
	Sort Descending		Sort rows in descending order in the Atom List Editor.
General icons used many places within GaussView:
	Move Up		Move the selected item up in a list.
	Move Down		Move the selected item down in a list.
	Add Selected		Add the selected item to a list.
	Add All		Add all items to a list.
	Remove Selected		Remove the selected item from a list.
	Remove all		Remove all items from a list.