Dear all, this is my first mail on the list, so what I am going to do is: I) try what i am trying to achieve II) what classes/methods I use Its fairly simple: I create a molecule and endow it with some structure using the provided PMI classes: s = System() st = s.create_state() m = st.create_molecule(molecule.name ,sequence=molecule.get_sequence(),chain_id=molecule.chain_id) for pdb_path,chain_id in molecule: struc = m.add_structure(pdb_path,chain_id,soft_check=True) m.add_representation(struc,resolutions=[0]) The "molecule" object is a convenience class that holds the necessary information. The other methods and objects are typical pmi elements. I create a clone, build the system and decorate the clone because I want to apply a transformation to it. I do that, afterwards i write the system to pdb: c = m.create_clone(molecule.chain_id+"_C") s.build() cx = IMP.core.XYZ(c.get_hierarchy()) IMP.core.transform(cx,g) IMP.atom.write_pdb(s.get_hierarchy(),"test_1.pdb") g rotates the clone around some axis specified elsewhere. When I look at the file I would expect two molecule in different positions, yet they sit on top of each other. What am I missing? Thanks in advance and all the best, Kai (Jans friend)