i have a pdb file

A pdb file is a file that contain a set of points in  3 dimensions (x,y,z) that describe a protein. It can be any shape. I must extract from this set of coordinates a surface file that is composed only of the coordinates that are outside from the shape. There is another problem: i musn't take care of the point that are on the surface but in an incurvation 

I ve got no idea how to start.  Thanks for helping me