The GaussView User Interface

Toolbars

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.

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 key modifier is the Command key, not the Control key.

Icon Name Menu Path Purpose Keystroke
i_new.tif New Molc. Group File=>New Mol. Group Create a new molecule (per submenu selection). Ctrl-N
i_addmol.tif Add to Molc. Group File=>New=>Add to Mol. Group Add a new molecule to the current molecule group. Ctrl-A
i_open.tif Open File=>Open Open files supported by GaussView. Ctrl-O
    File=>Recent Files 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 Maximum Recent Files field in the File/Directory preferences. The file list is saved across GaussView sessions.
    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.
i_save.tif Save File=>Save Save molecule(s) in the active molecule group to file(s). Ctrl-S
    File=>Save Temp Files Save any temporary files associated with Gaussian Quick Launch jobs.
    File=>Convert Files Convert between various Gaussian file and molecule file types.
    File=>Directory Opens the directory associated with file corresponding to the active molecule group in the native operating system. It also selects the file.
i_print.tif Print File=>Print Print the contents of the active View window. This selection opens the operating system’s print dialog. Ctrl-P
i_image.tif Save Image File=>Save
Image File
Produce a graphics file of the current View window.
i_movie.tif Save Movie File=>Save Movie Save movie file, movie frame files, or both (selected via submenu).
i_prefs.tif Preferences File=>Preferences Specify defaults for aspects of GaussView’s behavior.
    File=>Exit Close all GaussView windows and exit application.
i_undo.tif Undo Edit=>Undo Reverse the previous editing action, and maintain a list of all previous actions for potential Redo. Ctrl-Z
i_redo.tif Redo Edit=>Redo Reverse the previous Undo operation. Ctrl-Y
i_cut.tif Cut Edit=>Cut Cut the current selection to clipboard. Ctrl-X
i_copy.tif Copy Edit=>Copy Copy the current selection to clipboard. Ctrl-C
i_paste.tif 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.
i_delmol.tif Delete Edit=>Delete Remove the current selection. Del
i_imgcap.tif Image Capture Edit=>Image Capture Copy the contents of the active View window to the clipboard. Ctrl-I
i_stdz.tif Standardize Z-Matrix Edit=>Standardize Z-Matrix Rewrite the current Z-matrix in a standardized form.
i_symmetrize.tif Symmetrize Edit=>Symmetrize Apply point group symmetry to the current model.
    Edit=>Reorient Restore canonical molecule orientation.
i_rebond.tif Rebond Edit=>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 Edit=>Remove Weak Bonds Remove all weak bonds from the structure. Weak bonds are indicated by dashed lines between the atoms.
i_clean.tif 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.
i_atomlist.tif Atom List Editor Tools=>Atom List Edit the molecule’s numerical coordinates and parameters in a spreadsheet-like dialog.
i_redcoord.tif Redundant
Coord. Editor
Tools=>Redundant Coordinates Specify redundant internal coordinates for the Gaussian ModRedundant option.
i_conned.tif Connection
Editor
Tools=>Connection Specify corresponding atoms in two related molecular structures (e.g., for Opt=QST2 or QST3 input).
i_layers.tif Select Layer Tools=>Select Layer Assign atoms to layers graphically for ONIOM calculations.
    Tools=>Atom Groups Open the Atom Group Editor, useful for defining fragments, ONIOM layers, frozen atoms, and other atom groupings.
    Tools=>Atom
Selection
Open the Atom Selection Editor, enabling you to perform advanced selection operations.
    Tools=>PDB Residues Open the PDB Residue Editor, which enables operations based on residues as defined in the originating PDB file.
    Tools=>PDB Secondary Structures Open the PDB Secondary Structure Editor, which enables operations based on PDB file secondary structures (e.g., chains and helixes).
    Tools=>Point Group Specify/impose symmetry on the current model.
i_pbc.tif Crystal Editor Tools=>PBC Create and modify unit cells for periodic structures.
i_mo.tif MO Editor Tools=>MOs View, reorder, and modify occupancy for molecular orbitals.
    Tools=>Custom Bonding Parameters Specify alternate lengths for standard bond types.
i_element.tif Element Fragment Builder=>Element Fragment Open the Element Fragments palette.
i_ring.tif Ring Fragment Builder=>Ring Fragment Access a palette of ring structures.
i_group.tif R-Group Fragment Builder=>R-Group Fragment Summon a palette of functional group fragments.
i_amino.tif Biological Fragment Builder=>Biological Fragment Summon a palette of amino acid and nucleoside fragments.
i_mollib.tif Custom Fragment Builder=>Custom Fragment Access a custom fragment library.
  Fragment Builder=>Fragment Submenu displays a list of fragments of the checked type.
  Place Fragment at Centroid of Selected Atoms Builder=>Place Fragment at Centroid of Selected Atoms Places an atom at the centroid position of the currently selected atoms.
i_bond.tif Modify Bond Builder=>Modify Bond Access Bond SmartSlide dialog after two atoms are selected.
i_angle.tif Modify Angle Builder=>Modify Angle Access Angle SmartSlide dialog after three atoms are selected.
i_dihedral.tif Modify Dihedral Builder=>Modify Dihedral Access Dihedral SmartSlide dialog after four atoms are selected.
i_inquire.tif Inquire Builder=>Inquire Examine structural data for the current molecule.
i_addh.tif Add Valence Builder=>Add Valence Add an additional hydrogen to the selected atom.
i_delatom.tif Delete Atom Builder=>Delete Atom Eliminate atoms and/or open valences (dangling half bonds).
i_invert.tif Invert Atom Builder=>Invert Atom Invert molecular structure about a selected atom.
i_pick_click.tif Select Atoms by Clicking Builder=>Select Atoms by Clicking Select atoms by clicking on them.
i_pic_rubber.tif Select Atoms by Rubberband Builder=>Select Atoms by Rubberband Select atoms by clicking and dragging a marquee enclosing them.
i_pick_brush.tif Select Atoms by Brush Builder=>Select Atoms by Brush Select atoms by clicking and dragging a marquee enclosing them.
i_select_none.tif Deselect All Atoms Builder=>Deselect All Atoms Deselect all currently selected atoms.
i_select_all.tif Select All Atoms Builder=>Select All Atoms Select all atoms.
i_addview.tif Add View View=>Add View Create a new View window with an independently adjustable view of the current molecule.
i_center.tif 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.
i_display.tif Display Format View=>Display Format Specify the display format for molecules and surfaces. Ctrl-D
i_gcalc.tif 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
i_gquick.tif Quick Launch Calculate=>Gauss. Quick Launch Run a Gaussian job for the current molecule, bypassing the Gaussian Calculation Setup dialog.
i_gscheme.tif Schemes Calculate=>Gauss. Calc. Scheme Define and modify Gaussian calculation schemes.
  GMMX Conformer Dialog Calculate=>GMMX Conformer Dialog Perform a conformational search.
i_jobs.tif Current Jobs Calculate=>Current Jobs Display currently running GaussView-initiated Gaussian jobs (including CubeGen and FreqChk).
i_scjm.tif SC Job Manager Calculate=>SC Job Manager Open the SC Job Manager facility. 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=>PCM Solvation Cavity Display the IEFPCM solvation cavity for the Gaussian job.
    Results=>Atom Properties Display predicted atomic charges and other atom properties.
    Results=>Bond Properties Display predicted bond orders and other properties.
    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=>ORD Display predicted ORD spectra.
    Results=>Molecule Group Table Display results of one or more jobs in tabular form.
    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.
    Results=>Energy Plot Displays plots of energy conformations from GMMX calculations.
i_viewfile.tif View / Edit File Results=>View / Edit File Start an editor session for the log file for the current molecule.
i_stream.tif Stream Output File 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.
i_prev.tif Previous Windows=>Previous Activate the previous View window in sequence. PgUp
i_next.tif Next Windows=>Next Activate the next View window in sequence. PgDown
i_cascade.tif Cascade Windows=>Cascade Arrange all view windows in an overlapped pile.
i_tile.tif Tile Windows=>Tile Resize and rearrange view windows so that all are visible.
    Windows=>name Make the specified View window the active one.
i_help.tif Help Help=> GaussView Help Open the GaussView help facility. Ctrl-H
    Help=> Quick Start Essential information about building molecules, Gaussian job setup & running, and results visualization.
    Help=> Menus and Icons Reference table of all icons and menu items.
    Help=> How do I...? Frequently asked questions about GaussView.
    Help=> Tutorials List of GaussView tutorials.
    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.
i_info.tif   Help=>GaussView Tips Display GaussView tips.
i_fragplace.tif Fragment Placement   Open a panel containing fragment placement options within the control window.
Icons found in the Active Model View window:
i_animate.tif Animate   Display all models within the molecule group in succession.
i_stopani.tif Stop Animation   Stop an animated display.
i_view1.tif Single View   Display only one model within the molecule group.
i_viewn.tif Multi View   Display all models within the molecule group.
Icons found in the five Fragment Palette windows:
i_tacked.tif Tacked   Keep this palette open until explicitly closed (amodal operation).
i_notack.tif Untacked   Close palette when a different one is opened (modal operation).
Icons related to various coordinate editing dialogs:
i_zmat.tif Z-matrix Coordinates   Display Z-matrix coordinates.
i_cc.tif Cartesian Coordinates   Display Cartesian coordinates.
i_frac.tif Fractional Coordinates   Display fractional coordinates for periodic systems.
i_oniom.tif ONIOM Layers   Display ONIOM layer assignments and related data.
i_mm.tif MM Parameters   Display Molecular Mechanics atoms types and other data.
i_pdb.tif PDB Info   Display residue and chain assignments from a PDB file.
i_show_mass.tif Isotope Masses   Display column(s) containing isotopes mass(es).
Optimize Coordinate   Display columns specifying atoms freezing or optimization activation.
i_addcoord.tif Create a New Coordinate   Add a new redundant coordinate in the Redundant Coordinate Editor.
i_up.tif Sort Ascending   Sort rows in ascending order in the Atom List Editor.
i_down.tif Sort Descending   Sort rows in descending order in the Atom List Editor.
General icons used many places within GaussView:
i_up.tif Move Up   Move the selected item up in a list.
i_down.tif Move Down   Move the selected item down in a list.
i_sublist_1.tif Add Selected   Add the selected item to a list.
i_sublist_2.tif Add All   Add all items to a list.
i_sublist_3.tif Remove Selected   Remove the selected item from a list.
i_sublist_4.tif Remove all   Remove all items from a list.