A query with an R-group represents substitution variation on the same root structure.The molecule containing an R-group is the so called scaffold. An R-group query can involve several derivatives which 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: In order to create the definition for an R-group, firstly, 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 Context menu. See detailed description here.
Creating 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.
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.
Create them in Marvin JS: Atom Lists and NOT Lists can be defined using the Periodic Table.
Usage 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 etc.).For more details, please check the Atom page in the Drawing features section.
Built-in homology groups of Marvin JS represent series of chemical compounds with the same specific structural properties. Click here for the list of the available homology groups.
(If you need more information about the properties or search conditions of the homology groups, please, check the corresponding pages of JChem Base documentation or just click here. )
Create them 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.
Usage in Marvin JS: On the canvas you can manipulate the homology groups as other atoms (move, delete, overwrite etc.). For more details, please check the Atom page in the Drawing features section
Position variation bond represents a variable connection pointing from a group of atoms to an atom.
Create them in Marvin JS: Find these kind of bonds in the Bonds combo-box on the Tools toolbar. Detailed description how to draw position variation bond here.
Usage in Marvin JS: After creation, several properties of this bond is changeable, such as bond type, topology, location on the canvas, etc. You can see a detailed description about editing the bonds here.