General Toolbar - Top Toolbar

The general toolbar of Marvin JS consists of the icons below. Click the name of an icon to jump to the relevant section of the document.

Clear	Import	Export	Undo-Redo	Cut	Copy	Paste	Zoom	Clean 2D	Clean 3D	3D rotate	Auto Map	Calculate Stereo	Add/Remove explicit H	Aromatize and Dearomatize	View Settings	About Marvin JS

Clear

Keyboard shortcut: Ctrl+Delete.
Erases all structures from the canvas without saving. When the canvas is empty, the button is inactive, and after drawing on the canvas, it automatically activates.

Import

Keyboard shortcut: Ctrl+O.
Opens the Import dialog.

You can import a file from your file system by pushing the Choose File button or by pasting its source into the Paste source text field.

• Add: Appends the structure to the contents of the canvas.
• Replace: Overwrites the contents of the canvas with the new structure.

Export

Keyboard shortcut: Ctrl+S.
Opens the Export menu.

A structure can be saved either in ChemAxon Marvin Document format or in MDL Molfile V2000 format. To export in other file formats (SMILES, ChemAxon Extended SMILES, SMARTS, ChemAxon Extended SMARTS, InChI, InChIKey, IUPAC Name, CML, MDL Molfile V3000, MDL SDfile, ChemAxon Compressed Molfile, ChemAxon Compressed SDfile, XYZ, CDX, and SKC), the appropriate web service must be available.

The structure file format can be changed by selecting an option from the drop-down list of supported file formats.

To save that to a file, push the Download button at the bottom of the dialog window, click on the created link, and save the file with the preferred name and route. Alternatively, you can paste the structure source into a text editor and save it from there. In the case of CDX and SKC file formats, only the first option can be carried out.

In the Export menu, there is an option to save the structure as an image. The supported image formats are PNG and JPEG.

To save an image of the structure in Marvin JS, select the Image tab in the Export dialog. The default settings of image export are the same as they are in the View settings. You can set the display options, determine the color of the image background (transparent or white), and set the width and height of the image in pixels.

{primary} The transparent image background is only available for PNG format.

Undo-Redo

• Undo (Ctrl+Z): Revokes the last editing step.
• Redo (Ctrl+Y): This button is inactive until the Undo button is clicked. It restores the last undone editing step.

Cut

Keyboard shortcut: Ctrl+X.
Moves the selected structure to the clipboard.

Copy

Keyboard shortcut: Ctrl+C.
Creates a copy of the selected structure on the clipboard.

Paste

Keyboard shortcut: Ctrl+V.
Places the copied or cut structure onto the canvas.

Direct copy-paste between Marvin JS and other applications is available in MRV or MDL Molfile (V2000) formats without web services. If web services are available, direct copy-paste between Marvin JS and other applications are possible in every text formats.

{info} Please, note that in some browsers, copying and pasting the content from/to Marvin JS is possible only through keyboard shortcuts. In these browsers, after clicking the Cut, Copy, or Paste toolbar buttons, a message appears on the canvas.

Zoom

• Zoom in: Magnifies the structures on the canvas.
• Zoom out: Reduces the size of the structures on the canvas.
• Zoom all (Enter): Sets the optimal magnification to be able to view everything on the canvas.
• Zoom to selection (Ctrl+Enter): Increases the zoom ratio placing the selected object in the center. This tool is only available when there is an active selection on the canvas.

The zoom ratio can be changed by zooming with the mouse wheel. This function is browser-dependent.

The cleaning features are available only if the server connection is active, and the appropriate web service is available. Otherwise, the clean buttons will not appear.

Clean 2D

The cleaning features are available only if the server connection is active, and the appropriate web service is available. Otherwise, the clean buttons will not appear.

It calculates new 2D coordinates for the atoms on the canvas to get the same molecule in an evenly organized fashion. Partial cleaning of a structure is possible, too. If you have selected fragments of molecules or certain elements of a multimolecular structure, 2D cleaning affects only these selected objects.

Clean 3D

The cleaning features are available only if the server connection is active, and the appropriate web service is available. Otherwise, the clean buttons will not appear.

You can determine the 3D structure of your molecules by using the Clean 3D option on the General toolbar.

Rotate 3D

Rotates every molecule on the canvas in 3D.

To rotate molecules, follow the steps below:

1. Clicking on the canvas results that the molecule starts rotating automatically in 3D. You can stop the rotating by clicking again.
2. If you want to rotate the molecules in 3D manually, drag with the mouse pointer on the canvas. While rotating, you can see the current angle of rotation around the and horizontal (x- ) axis next to the cursor, as well as on the two axes at the edges of the canvas.
3. If you hold the Shift key while rotating, you can rotate the structure around the vertical or horizontal axis only, depending on the main direction of dragging (that is, if you move the cursor from left to right, the structure will be rotated around the y-axis, while if you drag the cursor up and down, the molecules will be rotated around the x-axis).
   

Auto Map

Assigns map numbers to the corresponding atoms in a reaction. Only active when there is one reaction arrow on the canvas. Works when the appropriate web service is available.

Calculate Stereo

Assigns the R or S label to a chiral center and the E or Z label to a double bond. The R/S and E/Z labels are determined through web service. In Marvin JS, both optical isomerism and geometric isomers can be determined with this tool.

Add-Remove Explicit Hydrogen

Adds or removes hydrogen atoms to/from the selected structure. Without selection, changes apply to every atom on the canvas. The appropriate web service must be set.

Aromatize and Dearomatize

• Aromatize: Transforms the molecule from Kekulé representation to aromatic representation by using the general aromatization method.
• Dearomatize: Transforms the molecule from aromatic representation to Kekulé representation. (This method does not check by default if Hückel's rule is valid.)

Pressing the button successively, the function converts the structure from Kekulé to aromatic form back and forth. If there is a selected aromatic ring on the canvas, aromatize and dearomatize method works only for the selected structural part. This tool requires JChem Web Services.

View Settings

Opens the View settings dialog, where structure display options can be modified.

About

Opens the About Marvin JS dialog, which contains the following information about the product:

• Marvin JS
• Build Date
• Licensed To
• Licensed Product
• Expiration Date
• Copyright