Draw out the section you would want to focus on and on either side define groups as X and Y; As a side note explain what X and Y stand for.

From my experience it is a quite easy thing to do with VMD (http://www.ks.uiuc.edu/Research/vmd/), using the molefacture plugin within VMD (http://www.ks.uiuc.edu/Research/vmd/plugins/molefacture/). All you have to do is finding the right bond you would like to rotate, and choose 4 atom (2 atom from the bonding part, and one atom from each of those 2), then modify the dihedral angle.

But if you never use it, then it'll probably take some time to learn how to use it.