Hello all, This seems like it should qualify as a bug. If I have an instance of iotbx_pdb_ext.input and I create a hierarchy with construct_hierarchy(), then I must retain the reference to that hierarchy or apparently I can never get it back:

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hierarchy = my_pdb.construct_hierarchy() def some_local_scope_function(a_pdb): local_hierarchy = a_pdb.construct_hierarchy() some_local_scope_function(my_pdb) […] RuntimeError: atom has another parent atom_group already.

Wouldn't better behavior just return the previously constructed hierarchy given that multiple hierarchies can't be made? If each atom apparently remembers to which atom_group it belongs (and presumably on up), then shouldn't it make sense that an iotbx_pdb_ext.input be able to remember it's own hierarchy and produce it upon demand? Looking at a iotbx_pdb_hierarchy_ext.root, I don't find a reference to the iotbx_pdb_ext.input from which it was created. So, although passing around a hierarchy might be the obvious work-around, the end-user still needs to do some accounting if said user wants to track which roots belong to which inputs, and vice versa. James