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)