Toolbars provide buttons for accessing the majority of the features offered by Marvin JS. The button of the currently selected tool has a grey frame to indicate its active status.
Hover a cursor over a button to see a tooltip describing the functionality of the button.
General Toolbar
The General toolbar contains buttons for file management (Import, Export) and for general editing/viewing of the canvas content (Clear, Undo/Redo, Cut/Copy/Paste, Zoom, Clean, Navigate and View Settings).
 |
Clear |
Clear the whole canvas without saving its content. |
 |
Import |
Load an already existing file into Marvin JS. See the supported file formats here. |
 |
Export |
Save your structures in the choosen file format. See the supported file formats here. |
 |
Undo |
Revert the last commands you applied. |
 |
Redo |
Revert the effect of the last "Undo" command. |
 |
Cut |
Place the selection on the clipboard, while removing the original structure from the canvas. |
 |
Copy |
Place the selection on the clipboard, while leaving the original structure unchanged. |
 |
Paste |
Insert the content of the clipboard onto the canvas. |
 |
Zoom in |
Increase the zoom ratio. |
 |
Zoom out |
Decrease the zoom ratio. |
 |
Zoom All |
Change the zoom ratio to the optimal value to view everything on the canvas. |
 |
Zoom to Selection |
The selected object will be the center of zooming. |
 |
Clean 2D |
Clean the structure(s) on the canvas in 2D by recalculating the atomic coordinates. |
 |
Clean 3D |
Clean the structure(s) on the canvas in 3D by recalculating the atomic coordinates. |
 |
Auto Map | Assigns map numbers to the corresponding atoms in a reaction. |
 |
Calculate stereo |
Determine R/S stereo labels for chiral atoms and E/Z labels for double bonds. |
 |
Add/Remove explicit H | Add/remove hydrogen atoms to/from the selected structure. Without selection changes apply for every atom on the canvas. |
 |
3D rotate |
Rotate your structure in 3D. |
 |
View Settings |
Set display properties in the View Settings dialog box. |
 |
About Marvin JS |
Displays information about the application (name, version number) and a link to the User's Guide. |
Tools Toolbar
The Tools toolbar offers several options for drawing or editing structures.
There are "combo" buttons on the Tools toolbar, which have a triangle in their lower right corner. When you click there, you can select a function from a list of options. Once an option is selected, the main "combo" button retains the selection.
|
Selection |
Select whole structures or molecule fragments. |
|
Delete |
Erase one or more structures or molecule fragments. |
|
Open the complete list of chemical bonds including several query bond types. |
|
|
Chain |
Draw an alkyl chain of arbitrary length. |
|
Abbreviated Groups |
Insert abbreviated groups. |
|
Increase Charge |
Increase the charge of an atom with one unit (i.e. adds a positive charge to the atom). |
|
Decrease Charge |
Decrease the charge of an atom with one unit (i.e. adds a negative charge to the atom). |
 |
Smart R-group | Insert an R-group or create an R-group definition. |
 |
R-group attachment | Add an R-group attachment point to an atom. |
 |
Straight Arrow | "Combo" button to select between single (straight) or two-headed (resonance) arrows. |
 |
Reaction Operator | Place a "+" sign between the reactants or products of a reaction. |
 |
Rectangle | "Combo" button to draw a graphical box (e.g. rectangle, ellipse ). |
 |
Electron Flow Operator | "Combo" button to select between single or double electron flow arrows. |
Bonds
You can choose any type of bond by clicking on the lower right corner of the Bonds "combo" button in the toolbar. Among these bonds you can find several query types, too. You can also use keyboard shortcuts to choose a bond type to connect two atoms or alter an already existing bond. See the complete list of chemical bonds available in Marvin for JavaScript and their respective keyboard shortcuts in the table below.
Bond symbol |
Bond type |
Shortcut |
|
Drawing |
|
|
"Single" bond |
1 |
|
"Double" bond |
2 |
|
"Triple" bond |
3 |
|
"Aromatic" bond |
4 |
|
"Single Up" wedge bond |
5 |
|
"Single Down" wedge bond |
6 |
|
"Single Up or Down" query bond |
7 |
|
"Double Cis or Trans" query bond |
- |
|
"Double C/T or Unspecified" query bond |
- |
|
"Single or Double" query bond |
12 |
|
"Single or Aromatic" query bond |
14 |
|
"Double or Aromatic" query bond |
24 |
|
"Any" query bond |
0 |
|
"Coordinate" bond |
- |
Atoms Toolbar
The elements of the Atoms toolbar provide tools for drawing and modifying atoms, including query atom types, too. The chosen atomic symbol appears on the tip of the cursor. After a left-click, this atom is put on the canvas. Note that you can also use shortcuts (atomic symbols) to choose any atom from the Periodic Table.
|
Open the Periodic Table to select an atom. |
|
|
Frequently used atoms |
The most frequently used atoms can be reached directly from the toolbar. |
|
Draw a '*' atom (e.g., for an unspecified end group in a polymer). |
|
|
"Combo" button to select a query atom type or define a pseudo atom. |
Periodic Table
This button opens the Periodic Table in a pop-up window. You can choose any atom from the Periodic Table to put it on the canvas with a left-click. You can also define Atom Lists and NOT Lists for query structures. The selected atom or list appears on the tip of the cursor, and you can place it on the canvas one or more times.
Star (*) atom
In most cases, a '*' atom stands for an unspecified end group in a polymer. More generally, it can symbolize any type of unknown or unspecified groups or molecules. Technically, it is an 'AH' type query atom (any elements including hydrogen) with an alias.
Query atoms
Marvin JS offers several query atom types, which can be reached by left-clicking on the lower right corner of the Query Atoms "combo" button. See the complete list in the table below. Pseudo atoms are also available from here.
|
Any of the elements except hydrogen |
|
Hetero atom (any atom except carbon and hydrogen) |
|
Metal atom |
|
Halogen atom |
|
Any of the elements including hydrogen |
|
Any of the elements except carbon |
|
Metal atom or hydrogen |
|
Halogen atom or hydrogen |
|
Pseudo atom |
Templates Toolbar
Five generic templates are available from the Templates toolbar. After selecting one of these templates you can place it on the canvas with a left mouse-click. When placing it on the canvas, you can rotate the template around its center by dragging the cursor. Templates can also be connected to already existing structures by sprout drawing.
|
Cyclohexane |
|
Cyclopentane |
|
Pyrrole |
|
Cyclopentane (house) |
|
Benzene |
