Tips for Using the Chemical Editor Marvin

Downloading Marvin

Marvin can be downloaded from The Marvin home page can be found at

You will need to register with ChemAxon in order to download Marvin. The download section can be found on the left hand panel of the home page, near the bottom of the screen. Once you have accepted the User License, you can register and then, download the software. The download section is under Marvin Beans and full instructions are available on the Marvin site.

Using Marvin

Full user instructions can be found on the Marvin site However, here are some essential tips...

Connecting Atoms

When you need to join two atoms together, select the bond tool and hover over the first atom. When you have the atom selected, a circle will appear around the atom. click on the atom then and hold the left mouse button down, select the atom that you wish to connect to then release the mouse button.

Changing Bonds

To remove a bond, simply right click on the bond. This will pull up a bond pop-up menu. Select, from this menu, remove bond.

To change a double bond to a single bond again use the bond pop-up menu. It is also possible just to select the bond tool and cycle through the various options Marvin will allow.

Changing Charges

To alter charges on an atom, either select the plus (+) or minus (-) drawing tools and click on the desired atom. These tools are on the middle row of drawing tools at the far left. Alternatively, go into selection mode and right click on the atom, under the atom pop-up menu there is a charge sub-menu, and charge can be altered here.

Implicit vs. Explicit Hydrogens

By default, Marvin displays implicit hydrogens. These can either be drawn in explicitly, or the option to display implicit hydrogens can be turned off. To turn off the implicit hydrogen display simply go to the View menu, the Hydrogens sub-menu and select the option to turn implicit hydrogens off.

A Note on R groups

It is known that if an R group is created in Marvin, the animation process will fail. This is due to the way Marvin creates its CML output. It is therefore recommended that R groups be avoided.

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