This article will guide you through the process of creating Markush structures for searching.
First, draw or search for the base structure you wish to search with.
Once the base structure is made, select the icon on the Marvin JS, this will allow you to select the atoms that would represent R1 or R2 and so on.
For example the below I have replaced the CH3 on the ring structure with an R1.
Once this is done you can then start to define the variables for the R-groups.
Select the atoms or draw a structure that you wish to be the variable.
Now use the R-Group Attachment button and apply them to the variables as shown below.
Once this is done, select the again and this time, click and drag to apply the grouping to the variable R-Groups.
If this is done correctly you will see an R1= icon appear as shown below.
You can then start your search and our platform will search for structures with the different R-Group variable selected.