Page tree

How to create reactions

How to put a "+" sign onto the canvas:

Select the Reaction tool, then left-click onto the canvas where you would like to place the "+" sign.

Plus on the Canvas

(lightbulb) If you select the reactant or the product side with the Selection tool and then press the Reaction tool button, the "+" sign(s) will be added automatically between each reactant or product molecule.

It works only if the selection does not contain other "+" signs or a reaction arrow.

Plus on the Canvas 2

How to put an arrow onto the canvas:

Select the Reaction tool, then drag with it on the canvas where you would like to place the arrow. During the dragging a gray feedback shows the future position of the newly forming arrow. Release the button to create the arrow.

If it is necessary the length and the direction of the arrow can be changed afterwards.

Draw Arrow

Reaction export - Technical details

  • If the structure on the canvas contains only a single step reaction, then it will be automatically exported as a "reaction file" by Marvin JS *.
    (This means that, in the exported file, there will be separate blocks for reactants, products and agents, making it possible to use the exported file in a reaction search.)
    In this case, only those file formats are available in the Export dialog which support reactions (MRV, RXN, SMILES, CXSMILES, SMARTS, CXSMARTS, CML, RXN V3000, SDF, CSSDF, CDX, SKC).

  • When the structure contains more than one reaction or a multistep reaction (or when the reaction converter web service is not available), the structure will not be converted into a reaction file.
    In this case, there will not be reactant/product/agent blocks in the exported files, and the "+" signs and arrows of the reaction(s) will be exported as text characters.

* Before Marvin JS 16.9.12, the conversion of the structure to a reaction file happened on the server side and required the reaction converter Web Service. You can try out this with the EXTERNAL property.

Display of reactions

Moving the Plus Sign

The Reaction operators are movable by dragging them on the canvas with active Selection tool.

How to delete reaction operators 

Deleting a Plus Sign

You can delete reaction operators by clicking on them with active Delete tool, or by selecting them, then pushing the Delete key.

Deleting an ArrowClicking on the middle of the arrows when the Smart reaction tool is active deletes the arrow.

Merged Agents

What is merged agent, when should you use it?

Merged agents represent a special grouping inside Marvin JS, which gives you the opportunity to handle structures together as one molecule in mrv format. This could be important when you need to visually indicate that separated structures belong together (for example salts) or if you need to use the mrv file in other softwares for example search.

How to create merged agents

Creating Merged Agents

Display of Merged agents

On hover squared brackets appear around the structures, and bonds and atoms in the group are indicated in grey.

How to remove merged agent group

Merged group is automatically removed if only one structural part remains in it, or if the group is moved to reactant or product position.

The grouping can be also removed, with Context menu Unmerge Agent(s) option.

Removing Merged Agent Group

Related pages