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)
