Menus of MarvinView

The Menu Bar contains almost all commands that are available in MarvinSketch.
The main menus are groups of functionally similar commands shown in the following picture:

File Menu

The File menu contains the available file operations, such as New, Open, Save, Print, and Close. (Note that the unsigned Swing applets contain only a subset of these functions.)

Edit Menu

The Edit menu contains general clipboard operations like Copy and Paste, and Marvin-specific editing options.

View Menu

The View menu allows you to alter the way the molecules are displayed. You can change the molecule display type, background color, color scheme, error highlighting, etc.

Table Menu

The Table menu offers different settings to set up the table in which molecules and the corresponding molecule data fields are displayed.

Structure Menu

Provides chemical functions relating to structures like molecule cleaning, aromatization, and more.

Tools Menu

Contains the available Calculator Plugins (except Services Plugin).

Help Menu

Provides information about using the program, technical details and license management.

Full Menu Reference

File Menu

Open	Loads a molecule file into Marvin and closes the molecules you were previously working with.
Recent Files	List of the recently used file names.
Save Selection	Saves the molecule being in the selected cell. If there is no cell selected, you can specify molecules to save by giving a single cell index or a range of cell indices.
Save All	Saves all molecules to a different location or with a different file name or format.
Save As Image	Save an image of the selected molecule in the required location in required format.
Print	Prints an image of either the current molecule, the visible molecules or all molecules.
Exit	Saves preferences and closes the application.

Edit Menu

Copy	Copies the selection to the clipboard.
Copy As	Copies the selection to the clipboard in the specified format.
Copy As SMILES	Copies the selection to the clipboard in SMILES format.
Paste	Inserts the contents of the clipboard at the location of the cursor, without replacing selection.
Find	Allows searching for an expression in the molecule data fields.
Find Again	Repeats the last search, highlighting the next match if it exists.
Structure	You can alter a molecule by editing it with MarvinSketch.
Source	You can alter a molecule by directly editing its source in the Edit Source Window. You can view and edit the source in any of the supported file formats.
Preferences	The Preferences dialog window allows you to change many of the MarvinView display settings, including look & feel, error highlighting, and object visibility.

View Menu

Transform > Translate or Drag	Shifts the structure on the canvas with the mouse.
Transform > Zoom	Zoom of the content of the canvas by dragging the mouse without modifying atom coordinates.
Transform > Rotate in 3D	Spin the structure around its central point in 3 dimension with the help of the mouse without modifying atom coordinates.
Transform > Rotate in 2D	Spin the structure around its central point in 2 dimension with the help of the mouse without modifying atom coordinates.
Transform > Zoom/Rotate	Uses the zoom transformation when the mouse is moved vertically and uses rotation when the mouse is moved horizontally.
Transform > Reset View	Restores the starting view as modified by rotation and zoom.
Animation > Play/Pause	Starts/stops an XYZ animation sequence, or starts rotating the selected molecule in 3D.
Animation > Rewind	Stops the animation and resets it to the starting position.
Animation > Quantize Spin	Changes the number of rotations from the current value to the closest integer, for example 1.8 rotation / 198 frames is changed to 2 rotations / 198 frames. The effect is irreversible.
Animation > Drag to Spin	Allows changing the direction and speed of the rotation using mouse dragging.
Display > Atom Symbols in 3D	Sets atom symbol visibility in 3D mode. Note that in 3D mode, atoms may become invisible in Wireframe and Stick mode by hiding atom symbols.
Display > Wireframe	Displays bonds as thin lines, and atoms (except Carbon) as symbols.
Display > Wireframe with Knobs	Displays bonds as thin lines, Carbon atoms as knobs, and other atoms as symbols.
Display > Sticks	Displays bonds as thick lines, and atoms (except Carbon) as symbols.
Display > Ball and Stick	Displays bonds as thick lines, atoms as shaded balls, and atoms (except Carbon and Hydrogen) as symbols on balls.
Display > Spacefill	Displays atoms as large shaded balls, and atoms (except Carbon and Hydrogen) as symbols on the balls.
Display > Quality > Low	Disables line anti-aliasing.
Display > Quality > High	Enables line anti-aliasing.
Colors > Monochrome	Displays all atoms with default drawing color.
Colors > CPK	Displays all atoms with Corey-Pauling-Kultun colors.
Colors > Shapely	This color scheme is based on RasMol's shapely color scheme for nucleic and amino acids.
Colors > Group	Coloring atoms based on PDB residue numbers.
Colors > Atom/Bond Sets	Colors atoms and bonds according to the color of the pre-defined set they belong to.
Colors > Background	Sets custom background color with adjusted default drawing color.
Colors > White Background	Sets the background color to white and the default drawing color to black.
Colors > Black Background	Sets the background color to black and the default drawing color to white.
Stereo > R/S Labels > All	Always show atom chirality (R/S).
Stereo > R/S Labels > Absolute Stereo	Show atom chirality if chiral flag is set for the molecule or the atom's enhanced stereo type is absolute.
Stereo > R/S Labels > None	Do not show atom chirality (R/S).
Stereo > E/Z Labels	Toggles the display of absolute double bond stereo configuration labels. Bonds known to have an (E) or (Z) configuration will be marked as such.
Stereo > Absolute Labels	Toggles the display of the Absolute label if the chiral flag is set on the molecule.
Implicit Hydrogens > On All	View hydrogens by symbol on all atoms. This option is disabled in Spacefill and Ball & Stick display modes.
Implicit Hydrogens > On Hetero and Terminal	View hydrogens by symbol on hetero and terminal carbon atoms. This option is disabled in Spacefill and Ball & Stick display modes.
Implicit Hydrogens > On Hetero	View hydrogens by symbol on hetero atoms only. This option is disabled in Spacefill and Ball & Stick display modes.
Implicit Hydrogens > Off	Disable hydrogens by symbol on all atoms.
Misc > Atom Numbers	Toggles the visibility of unique internal atom indices. The indices are continuous starting from 1.
Misc > Atom Properties	Toggles the visibility of atom properties.
Misc > Atom Mapping	Toggles the visibility of atom mapping labels.
Misc > Graph Invariants	Toggles the display of graph invariants (canonical labels).
Misc > Bond Lengths	Toggles the display of bond lengths in Angstroms on the middle of the bonds.
Misc > Lone Pairs	Toggles the display of lone pairs.
Misc > R-groups	Toggles the display of R-group definitions.
Misc > R-Logic	Toggles the display of R-logic definitions.
Misc > Valence	Toggles the display of valence numbers. Default setting is On.
Misc > Ligand Error	Toggles the display of ligand error. Default setting is On.
Rescale Cells > Separately	Changes the zoom of each cells individually so that molecules best fit their own cell.
Rescale Cells > Uniformly	Changes the zoom ratio of all cells to the same value with which all molecules are fully visible in their own cell.
Open MarvinSpace	Launches a MarvinSpace window containing the current molecule from the Sketcher.

Table Menu

Options	Allows configuration of the table in which molecules are displayed.
Show Fields	Shows all available molecule data fields.
Show Molecule Name	Shows the name of the molecules if they are available.
Show Generated Name	Generates IUPAC name for the molecules and displays them.
Show SMILES	Shows the SMILES representation of the molecules.

Structure Menu

Clean 2D > Clean in 2D	Calculates new 2D coordinates for the molecule.
Clean 2D > Clean Wedge Bond	Adds an explicit hydrogen atom to a chiral center having no terminal atoms when 2D cleaning is performed.
Clean 3D > Clean in 3D	Calculates new 3D coordinates for the molecule. Clean3D builds up conformers of fragments from which the best, i.e. the lowest energy conformer is given back. The quality of the structures is measured by a simple energy function (Dreiding type molecular mechanics).
Clean 3D > Cleaning Method > Fine Build	Fine Clean3D builds up conformers of fragments to find low energy conformer. Leaves failed fragments intact.
Clean 3D > Cleaning Method > Fine with Hydrogenize	The build process always adds explicit Hydrogens to the structures which are removed if not present in the original molecule. This option prevents the removal of extra Hydrogen atoms, otherwise gives the same results than Fine build.
Clean 3D > Cleaning Method > Fast Build	Fast clean, which if fails, performs fine clean. It accepts any generated structure, and it is the default behavior of the Clean3D function.
Clean 3D > Cleaning Method > Build or Optimize	Builds 3D structure for non-3D molecules and just optimizes the 3D molecules with the Dreiding force field.
Clean 3D > Cleaning Method > Gradient Optimize	Optimizes with the Dreiding force field using the actual structure as starting geometry.
Clean 3D > Display Stored Conformers	Allows you to choose one of the possible conformer structures which were calculated via the Conformers plugin.
Add > Explicit H Atoms	Adds explicit H atoms instead of the current implicit ones. Explicit hydrogens are displayed with atoms joining its neighbor while implicit hydrogens are displayed by atom symbols only.
Remove > Explicit H Atoms	Removes explicit H atoms and increases the number of implicit hydrogens.
Aromatic Form > Convert to Aromatic Form	Transforms the molecule to aromatic representation using the transformation method set.
Aromatic Form > Conversion Method > Basic	Basic conversion method is described here.
Aromatic Form > Conversion Method > General	General conversion method is described here.
Aromatic Form > Conversion Method > Loose	Loose conversion method is described here.
Aromatic Form > Convert to Kekulé Form	Transforms the molecule to non-aromatic representation.
Groups > Contract Group	Contracts all groups to its abbreviations.
Groups > Expand Group	Displays the full structure instead of the abbreviations.
Regenerate Bonds	Generate bonds for an XYZ structure with a different bond length cut-off.

Help Menu

Help Contents	Shows MarvinView User's Guide.
Licenses	Starts ChemAxon License Manager where you can manage the licenses of all ChemAxon products.
About MarvinView	Shows MarvinView product information and technical details.