A query with an R-group represents substitution variation on the same root structure. The molecule containing an R-group is called a scaffold. An R-group query can involve several derivatives that differ in one or more substituents (fragments).
Managing R-groups: Change the number by clicking repeatedly with the Smart R-group tool; change the label and add other properties in the Atom Properties menu.
Creating R-group definitions in Marvin JS: To create the definition for an R-group, first, draw the substituents from which the R-group should stand for, then enframe them with the Smart R-group tool or after selection use the R+Space keyboard shortcut.
Modify R-group definitions: You can manipulate the R-group definitions by the Smart R-group tool or by the context menu. See the detailed description here.
Creating an R-group attachment point in Marvin JS: You can add attachment points to the fragments in an R-group definition by using the R-group Attachment button or from the context menu. The attachment points on every separate fragment are automatically numbered beginning with 1.
Change attachment's properties: The bond type of the R-group attachment points can be changed using either the R-group attachment point tool or any of the bond tools.
R-group definition import and export are supported only in ChemAxon Marvin Document (MRV) format in Marvin JS; besides, you can choose other formats if the relevant web service is available.
Creating R-logic in Marvin JS: Adding R-logic to an R-group query is possible via R-logic Dialog, which is available from the Empty space, the Atom, and also the R-label context menus if there is at least one R-group definition on the canvas.
Modify R-logic: You can do any modifications in the R-logic Dialog.
Atom Lists and NOT Lists
An atom list query atom indicates any atom that is part of the list; similarly, a NOT list query atom can represent any atom that is not part of the list.
Creating atom lists and NOT lists in Marvin JS: Atom Lists and NOT Lists can be defined using the Periodic Table.
Using atom lists and NOT lists in Marvin JS: After creation, you can modify the elements in Atom properties dialog, otherwise, you can handle them as other atoms (move, delete, overwrite, and so on). For more details, please check the Atom page in the Drawing features section.
Built-in homology groups of Marvin JS represent a series of chemical compounds with the same specific structural properties. For a list of the available homology groups, see Atom Properties Dialog.
For more information about the properties or search conditions of the homology groups, see Homology Groups and Markush Structures.
Creating homology groups in Marvin JS: Homology groups can be created via Atom properties dialog, after a right-click on an atom. At the top of the dialog, change 'Element' to 'Homology Groups' then select the appropriate group from the list and choose either its full name or its alias at the 'Display' option.
Using homology groups in Marvin JS: On the canvas, you can manipulate the homology groups as other atoms (move, delete, overwrite, and so on). For more details, please check the Atom page in the Drawing features section
Position Variation Bond
The position variation bond represents a variable connection pointing from a group of atoms to an atom.
Using position variation bond in Marvin JS: After creation, several properties of this bond are changeable, such as bond type, topology, location on the canvas, and so on.