My name is Merav and I am working with the modeling with EM and cross links. I started from the example  with rnapolii.

I have attached my topology file. I have one PDB that contains 3 proteins and should be one rigid body (ARP7, ARP9, RT102). I also have one protein with 3 subunits that should be 3 rigid bodies (RCS2_1, RCS2_2, RCS2_3) and should belong to the super rigid body.
What would be the right way to specify that in the topology file? or should it be done in the script like in rnapolii example (which is not clear either)?