Hi everyone, I am quite new here (I have been reading your post in past...) and now I decide to post a question (easy maybe). I couldn't find any answer on Google. I have got two complexes of (protein+ligand)1 and (protein+ligand)2 where the only difference between the two is the different orientation of the ligand. My purpose is to overlay the protein (or maybe better the binding site) and to calculate the rms of the ligand's mismatch. The pdb file contains the protein+ligand. Do I need to create the ligand object for doing that? I aware that is a common task...sorry for the silly start :P
andrea
