Toolbars of MarvinSketch

Note: Place the mouse cursor over a toolbar button to see the tooltip describing its use.

General Toolbar

	Rectangle Selection	Allows selection in rectangle mode on mouse drag.
	Lasso Selection	Allows selection in lasso mode on mouse drag.
	Structure Selection	Allows selection in structure selection mode on mouse drag. With this selection mode only whole fragments can be selected.
	Erase	Removes all structures upon selection.
	Undo	Reverses the last command or the last entry you typed.
	Redo	Reverses the action of the last Undo command.
	Cut	Removes and copies the selection to the clipboard.
	Copy	Copies the selection to the clipboard.
	Paste	Inserts the contents of the clipboard at the location of the cursor, without replacing selection.
	Check Structure	Checks and corrects chemical structures. See Structure Checker in MarvinSketch for more details.
	Zoom In	Increases the canvas's magnification.
	Zoom Out	Decreases the canvas's magnification.
	Zoom Tool	Changes the canvas's magnification to a specific value. It can also do autoscale using named values: All, Selection, Scaffold, R-groups.
	Help Contents	Shows MarvinSketch User's Guide.

Tools Toolbar

The tools consist of various command groups. The tools having chemical meaning (like bond or reaction arrow) are drawn in black lines, while strictly graphical objects are in blue. You can place for example only ONE reaction arrow on the canvas, but as many graphical arrows as you wish and they will look completely identical.

	Insert Bond	Places various bond types on the canvas.
	Insert Chain	Places a carbon chain on the canvas. The number of carbon atoms can be increased or decreased by dragging the mouse. Selection of straight or curved chain drawing is available.
	Bold Tool	Thickens the selected bond. See details on bold tool function.
	Hashed Bond Tool	Makes the selected bond hashed. It only retains single original bond type.
	Insert Text	Places a Text object on the canvas. Allows changing text properties on the appearing toolbar.
	Insert Reaction Arrow	Places various reaction arrow objects on the canvas.
	Create Group	Creates a custom abbreviation group.
	Insert Brackets	Places brackets, parentheses, chevrons or braces on the canvas.
	Insert Graphics	Places various graphical objects on the canvas.
	Increase Charge	Increases the charge of the selected atom. The number of implicit hydrogens will be adjusted if possible to accommodate the new charge. Valence errors will be highlighted in red.
	Decrease Charge	Decreases the charge of the selected atom. The number of implicit hydrogens will be adjusted if possible to accommodate the new charge. Valence errors will be highlighted in red.

Atoms Toolbar

	Periodic System	Shows periodic system and query/atom property drawing window.
	Insert Hydrogen	Places Hydrogen atom on the canvas.
	Insert Carbon	Places Carbon atom on the canvas.
	Insert Nitrogen	Places Nitrogen atom on the canvas.
	Insert Oxygen	Places Oxygen atom on the canvas.
	Insert Sulfur	Places Sulfur atom on the canvas.
	Insert Fluorine	Places Fluorine atom on the canvas.
	Insert Phosphorus	Places Phosphorus atom on the canvas.
	Insert Chlorine	Places Chlorine atom on the canvas.
	Insert Bromine	Places Bromine atom on the canvas.
	Insert Iodine	Places Iodine atom on the canvas.

Chemical Toolbar

	Clean 2D	Calculates new 2D coordinates for the molecule.
	Clean 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).
	Convert to Aromatic Form	Transforms the molecule to aromatic representation using the transformation method set.
	Convert to Kekulé Form	Transforms the molecule to non-aromatic representation.

Markush Toolbar

	Position Variation Bond	Creates a variable point of attachment to represent a connection point to a group of atoms.
	Frequency Variation	Creates a Repeating Unit with Repetition Ranges.
	R-group attachment	Adds an attachment to the structure.

Advanced Templates Toolbar

1. The toolbar can show different template groups.
   • General and My Templates:
     
     
   • Crown Ethers and Bridged Polycyclics:
     
     
   • To control which template sets are displayed on the toolbar, use the Properties panel in the Template Library (Ctrl+t):
     
     
   Checking the 'Use molecules as templates at 2D cleaning' checkbox will effect the structures containing that template during cleaning of the structure: the default cleaning form is overwritten by the template structure. This way, you can cutomize your drawings: add or draw a set of templates and check this option.
2. Any structure can be added to the My Templates group.
   • Using Drag & Drop to the toolbar
     
   • Using the Pop-up menu
     
3. Set the name of the new template.
   • Right-click on the template icon on the template toolbar and select Properties.
   • Set the name and/or the abbreviation of the template in the Template Properties box.
   • After that the template is identified with its name and/or abbreviation.
     
4. Templates without a name
   • If the template does not have a name, hovering the cursor over its icon on the template toolbar magnifies the image on the icon. This improves the visibility of the template icon, especially for big structures.
     
5. The template can be removed from the toolbar.
   • Right-click on the template icon and select Remove to remove the template from the toolbar and from the My Templates list.

Simple Templates Toolbar

	Cyclopentane (house)
	Pyrrole
	Cyclopentane
	Cyclohexane
	Benzene
	Naphthalene

3D editing Toolbar

	Maps atoms to merge.
	Merges assigned atoms.
	Alters the coordinates of the molecule in order to put the 3 selected atoms of the molecule onto the plane of the canvas.
	Adds new fragment to the canvas.