We ran the script with the topology file that we attached, but all the domains don't move at all. 
Furthermore, we didn't understand the syntax of the 'super rigid bodies' coulmn, in the tutorial they use  2 numbers separated with a comma, but what do they refer to?  
Thanks again,

On Tue, Oct 24, 2017 at 3:38 AM, Ben Webb <ben@salilab.org> wrote:
On 10/23/17 12:43 AM, מירב בריטברד wrote:
*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)?

It depends on whether you are using PMI 1 or PMI 2.

For PMI 1 (using the BuildModel macro) specify the components you want in each rigid body and super rigid body in your Python script.

For PMI 2 (using the BuildSystem macro) use the relevant columns in the topology file. In order for two components to be in the same rigid body, you should use the same number in the rigid body column. Looks like you have that right for rigid bodies already.

ben@salilab.org                      https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
        - Sir Arthur Conan Doyle