Creating Reactions in Marvin JS: With Reaction tool you can draw "+" signs, arrows, and you also can map the reactions. You can read detailed description about the creation in the Reaction page in Drawing features section. (For more information about mapping see below.)
Multi-step reactions and graphical charts also can be created by the Reaction tool.
Reaction export - Technical details
* Please note that the conversion of the structure to a reaction file happens on server side and requires the reaction converter Web Service to be available.
See more technical information here: Reaction handling in Marvin JS (FAQ)
Marvin JS provides the option to set map numbers to individual atoms. Unlike atom indices, map numbers remain constant during editing the molecule. Mapping can be useful if you want to identify corresponding atoms in the reactant and product side of a reaction.
Creating and maintaining map numbers in Marvin JS: There are two ways for adding map numbers to the atoms.You can add map number to every single atom manually from the Atom properties dialog or if you would like to map the same atom with the same number, you can map these atoms by dragging from atom to atom when the Reaction tool is active. Both way are suitable for changing, or deleting the corresponding numbers.
Click the Auto Map button. In this case every atom in the reaction would get atom map number automatically.
Marvin JS supports the detailed display of reaction mechanisms by using electron flow arrows (or mechanism arrows) to describe the formation and breaking of chemical bonds.
Electron flow arrows describes the movement of electrons in the elementary reaction steps of a complex mechanism.
In Marvin JS, you can choose between two types of electron flow arrows:
|Single ()||Visualizing a single electron movement.|
|Double ()||Displaying the movement of electron pairs.|
Creation of curved arrows: If you want an atom to be the source of an electron flow arrow, the atom has to have a radical electron or a lone pair. Lone pair visibility should be switched on.
Manage the arrows in Marvin JS: You can change the position, the size, and the type (simple, incipient bond) of the arrows after creation. See details here.