[Chimera-users] zone command

A polypeptide was docked onto a protein that already carried ligands. Then, molecular dynamics of the complex was carried out. To do this, a single PDB file was created with the program ptraj of Amber. Although ptraj removes chain labels, TER lines, etc., renumbering all the residues in a single sequence, I know, from the ligand positions, the corresponding numbering for the chains and for the polypeptide. Which is the best procedure to map around certain groups of amino acids of the protein, i.e., those that constitute the experimentally-evaluated binding site? I want to take notice of which residues of the polypeptide are most involved in the binding. Thanks francesco pietra