The GaussView User Interface
The following illustrations show the GaussView toolbars and Builder palette. Consult the table following for the uses of the various icons.
GaussView Toolbars and Builder Palette
The main window toolbars are shown in standalone
mode.
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 key modifier is the Command key, not the Control key.
Icon | Name | Menu Path | Purpose | Keystroke |
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New Molc. Group | Create a new molecule (per submenu selection). | ||
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Add to Molc. Group | Add a new molecule to the current molecule group. | ||
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Open | Open files supported by GaussView. | ||
This menu path contains a list of files that have been opened most recently. You can specify the number of items in the list with the field in the preferences. The file list is saved across GaussView sessions. | ||||
List of files related to the current molecule (e.g., input file, log file, checkpoint file, etc.). | ||||
Reload current file in active View window. | ||||
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Save | Save molecule(s) in the active molecule group to file(s). | ||
Save any temporary files associated with Gaussian Quick Launch jobs. | ||||
Convert between various Gaussian file and molecule file types. | ||||
Opens the directory associated with file corresponding to the active molecule group in the native operating system. It also selects the file. | ||||
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Print the contents of the active View window. This selection opens the operating system’s print dialog. | |||
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Save Image | Produce a graphics file of the current View window. | ||
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Save Movie | Save movie file, movie frame files, or both (selected via submenu). | ||
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Preferences | Specify defaults for aspects of GaussView’s behavior. | ||
Close all GaussView windows and exit application. | ||||
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Undo | Reverse the previous editing action, and maintain a list of all previous actions for potential Redo. | ||
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Redo | Reverse the previous Undo operation. | ||
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Cut | Cut the current selection to clipboard. | ||
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Copy | Copy the current selection to clipboard. | ||
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Paste | Copy clipboard contents to the current model (per submenu selection). | ||
Add the molecule on the clipboard as a new model within the current model group. | ||||
Replace current molecule with clipboard contents. | ||||
Add molecule on the clipboard to the current model as a separate fragment. | ||||
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Delete | Remove the current selection. | ||
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Image Capture | Copy the contents of the active View window to the clipboard. | ||
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Standardize Z-Matrix | Rewrite the current Z-matrix in a standardized form. | ||
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Symmetrize | Apply point group symmetry to the current model. | ||
Restore canonical molecule orientation. | ||||
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Rebond | Initiates a rebonding process in which GaussView reidentifies bonded atoms, based on a distance algorithm. Note that Gaussian usually does not use the bond information on the screen for calculations. This information is presented primarily to make it convenient for you to visualize the chemistry of the molecule. | ||
Remove Weak Bonds | Remove all weak bonds from the structure. Weak bonds are indicated by dashed lines between the atoms. | |||
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Clean | Adjust molecular geometry according to a set of rules designed to match chemical intuition. | ||
Invert the molecule around the selected atom. | ||||
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Atom List Editor | Edit the molecule’s numerical coordinates and parameters in a spreadsheet-like dialog. | ||
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Redundant Coord. Editor |
Specify redundant internal coordinates for the Gaussian ModRedundant option. | ||
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Connection Editor |
Specify corresponding atoms in two related molecular structures (e.g., for Opt=QST2 or QST3 input). | ||
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Select Layer | Assign atoms to layers graphically for ONIOM calculations. | ||
Open the Atom Group Editor, useful for defining fragments, ONIOM layers, frozen atoms, and other atom groupings. | ||||
Open the Atom Selection Editor, enabling you to perform advanced selection operations. | ||||
Open the PDB Residue Editor, which enables operations based on residues as defined in the originating PDB file. | ||||
Open the PDB Secondary Structure Editor, which enables operations based on PDB file secondary structures (e.g., chains and helixes). | ||||
Specify/impose symmetry on the current model. | ||||
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Crystal Editor | Create and modify unit cells for periodic structures. | ||
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MO Editor | View, reorder, and modify occupancy for molecular orbitals. | ||
Specify alternate lengths for standard bond types. | ||||
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Element Fragment | Open the Element Fragments palette. | ||
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Ring Fragment | Access a palette of ring structures. | ||
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R-Group Fragment | Summon a palette of functional group fragments. | ||
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Biological Fragment | Summon a palette of amino acid and nucleoside fragments. | ||
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Custom Fragment | Access a custom fragment library. | ||
Fragment | Submenu displays a list of fragments of the checked type. | |||
Place Fragment at Centroid of Selected Atoms | Places an atom at the centroid position of the currently selected atoms. | |||
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Modify Bond | Access Bond SmartSlide dialog after two atoms are selected. | ||
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Modify Angle | Access Angle SmartSlide dialog after three atoms are selected. | ||
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Modify Dihedral | Access Dihedral SmartSlide dialog after four atoms are selected. | ||
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Inquire | Examine structural data for the current molecule. | ||
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Add Valence | Add an additional hydrogen to the selected atom. | ||
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Delete Atom | Eliminate atoms and/or open valences (dangling half bonds). | ||
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Invert Atom | Invert molecular structure about a selected atom. | ||
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Select Atoms by Clicking | Select atoms by clicking on them. | ||
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Select Atoms by Rubberband | Select atoms by clicking and dragging a marquee enclosing them. | ||
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Select Atoms by Brush | Select atoms by clicking and dragging a marquee enclosing them. | ||
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Deselect All Atoms | Deselect all currently selected atoms. | ||
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Select All Atoms | Select all atoms. | ||
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Add View | Create a new View window with an independently adjustable view of the current molecule. | ||
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Center | Center molecule in the View window (adjusts size). | ||
Close or reopen the standalone Builder palette. | ||||
Control the display of hydrogens in View window. | ||||
Control the display of dummy atoms in View window. | ||||
If selected, label each atom with its serial number (reflecting its sequence in the list of atoms). | ||||
If selected, display the chemical symbol for each atom. | ||||
Control the display of bonds in the View window. | ||||
Link views to synchronize mouse-based manipulations. | ||||
Control the display of X,Y,Z axes in the View window. | ||||
Indicate molecule’s stereochemistry by labeling relevant atoms as R or S. | ||||
Display the molecule positioning tools icons in the View window toolbar. | ||||
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Display Format | Specify the display format for molecules and surfaces. | ||
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Calculation | Set up Gaussian input for the molecular structure in the current view winodw and optionally run the job. | ||
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Quick Launch | Run a Gaussian job for the current molecule, bypassing the Gaussian Calculation Setup dialog. | ||
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Schemes | Define and modify Gaussian calculation schemes. | ||
GMMX Conformer Dialog | Perform a conformational search. | |||
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Current Jobs | Display currently running GaussView-initiated Gaussian jobs (including CubeGen and FreqChk). | ||
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SC Job Manager | Open the SC Job Manager facility. | ||
Provide summary data of the results of a Gaussian calculation (after a results file is opened). | ||||
Display partial charge density, as computed by various Gaussian methods. | ||||
Display the IEFPCM solvation cavity for the Gaussian job. | ||||
Display predicted atomic charges and other atom properties. | ||||
Display predicted bond orders and other properties. | ||||
Create, load, save, and display surfaces and contours. | ||||
Display calculated vibrational and other spectral data, including normal mode animation. | ||||
Display calculated NMR spectra. | ||||
Display predicted UV/Visible spectra. | ||||
Display predicted ORD spectra. | ||||
Display results of one or more jobs in tabular form. | ||||
Display plots of potential energy surface scans. | ||||
Display plots of predicted IRC paths. | ||||
Display trajectory plots from ADMP or BOMD calculations. | ||||
Display plots of geometry-optimization results. | ||||
Displays plots of energy conformations from GMMX calculations. | ||||
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View / Edit File | Start an editor session for the log file for the current molecule. | ||
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Stream Output File | Display output from a currently running Gaussian calculation continuously as it becomes available. | ||
Display/restore windows for all model groups. | ||||
Hide windows for all model groups. | ||||
name | Display/restore windows for the specified model group | |||
Minimize all view windows. | ||||
Raise active View window. | ||||
Open all minimized view windows. | ||||
Close the active View window. | ||||
Close all open view windows. | ||||
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Previous | Activate the previous View window in sequence. | ||
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Next | Activate the next View window in sequence. | ||
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Cascade | Arrange all view windows in an overlapped pile. | ||
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Tile | Resize and rearrange view windows so that all are visible. | ||
name | Make the specified View window the active one. | |||
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Help | Open the GaussView help facility. | ||
Essential information about building molecules, Gaussian job setup & running, and results visualization. | ||||
Reference table of all icons and menu items. | ||||
Frequently asked questions about GaussView. | ||||
List of GaussView tutorials. | ||||
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. | ||||
Display the GaussView copyright and version information. | ||||
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Display GaussView tips. | |||
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Fragment Placement | Open a panel containing fragment placement options within the control window. | ||
Icons found in the Active Model View window: | ||||
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Animate | Display all models within the molecule group in succession. | ||
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Stop Animation | Stop an animated display. | ||
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Single View | Display only one model within the molecule group. | ||
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Multi View | Display all models within the molecule group. | ||
Icons found in the five Fragment Palette windows: | ||||
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Tacked | Keep this palette open until explicitly closed (amodal operation). | ||
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Untacked | Close palette when a different one is opened (modal operation). | ||
Icons related to various coordinate editing dialogs: | ||||
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Z-matrix Coordinates | Display Z-matrix coordinates. | ||
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Cartesian Coordinates | Display Cartesian coordinates. | ||
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Fractional Coordinates | Display fractional coordinates for periodic systems. | ||
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ONIOM Layers | Display ONIOM layer assignments and related data. | ||
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MM Parameters | Display Molecular Mechanics atoms types and other data. | ||
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PDB Info | Display residue and chain assignments from a PDB file. | ||
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Isotope Masses | Display column(s) containing isotopes mass(es). | ||
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Optimize Coordinate | Display columns specifying atoms freezing or optimization activation. | ||
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Create a New Coordinate | Add a new redundant coordinate in the Redundant Coordinate Editor. | ||
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Sort Ascending | Sort rows in ascending order in the Atom List Editor. | ||
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Sort Descending | Sort rows in descending order in the Atom List Editor. | ||
General icons used many places within GaussView: | ||||
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Move Up | Move the selected item up in a list. | ||
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Move Down | Move the selected item down in a list. | ||
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Add Selected | Add the selected item to a list. | ||
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Add All | Add all items to a list. | ||
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Remove Selected | Remove the selected item from a list. | ||
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Remove all | Remove all items from a list. |