Set the position of SAMs on gold nanoparticle

Hello all,

I want to study the SAMs on the gold nanoparticle by MS. After I built the model of gold surface and an alkanethiol, I had two questions:

First, from the paper I know the SAMs on gold surface should be arraged like this Capturej.PNGwith specific angles shown in picture. I wonder how to set the position of SAMs on gold surface in MS.

Second, after I used build layers functions to put SAMs on the gold surface, it seemed that SAMs and gold surface can not be operated separetely and must move and rotate together. I wonder how to set the position of SAMs now?

Thank you so much!