Reaction

Create Reactions

Place a + Sign

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

If you select the reactant or the product side with the Selection tool and then press the Reaction tool button, the + signs are added automatically between each reactant or product molecule.

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

images/download/attachments/1802977/Plus_Sign_on_the_Canvas_2.png

Place an Arrow

Select the Reaction tool, then drag with it on the canvas where you would like to place the arrow. During the dragging, gray feedback shows the 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 afterward.

images/download/attachments/1802977/Draw_Arrow.png

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 are separate blocks for reactants, products, and agents, making it possible to use the exported file in a reaction search.

In this case, only file formats that support reactions are available in the Export Dialog (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 Reactions

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

images/download/attachments/1802977/Moving_the_Plus_Sign.png

Delete Reaction Operators

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

images/download/attachments/1802977/Deleting_a_Plus_Sign.png

Clicking the middle of the arrows when the Reaction tool is active deletes the arrow.

images/download/attachments/1802977/Deleting_an_Arrow.png

Merged Agents

Merged agents represent a special grouping inside Marvin JS, which allows you 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 software.

Create Merged Agents

images/download/attachments/1802977/Creating_Merged_Agents.png

Display Merged Agents

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

Remove Merged Agent Group

The 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 the Unmerge Agent(s) action that is available from the context menu.

images/download/attachments/1802977/Removing_Merged_Agent_Group.png