Hi,

I am trying to sample a PDB with different restraints. I would like to shuffle only some molecules, in order to have some of them in a fixed position (the coordinates should not change after sampling). I define these rigid particles as rigid bodies before shuffling, and suffling as:

IMP.pmi.tools.shuffle_configuration(root_hierarchy,
                                    excluded_rigid_bodies=fixed_particles,
                                    max_translation=50,
                                    verbose=True,
                                    cutoff=5.0,
                                    niterations=100)

- Fixed particles change their coordinates after shuffling.

- In the PDB (4 chains "ABCD"), the chains appear disconnected, even if I apply connectivity restraint.

I may do something wrong, any help would be appreciated!

Thanks!

Altair