I try to render a protein molecule to a geometry format (from .pdb format to .obj format) by Chimera. I use 'Multiscale models' tool in 'Higher-Order Structure' choice and then make the model by resurfacing at some appropriate resolution. It turns out that the whole protein molecule can be modeled pretty nicely. 

However, I now have a similar problem; instead of rendering the whole protein molecule, I would like to render the whole structure separately. I want to render the exposed residues (those residues on the surface) and non-exposed/buried residues separately, so I will have two obj files (one for the exposed residues and the others for the non-exposed residues).

I haven't been able to figure this problem out yet. Thus, I am wondering could you please give me some direction? Any advice will be greatly appreciated!

Thank you,

Hsin-Yi (Cindy) Yeh