Handle non-atom nodes more completely in rmf_pdb

[benmwebb]

Currently rmf_pdb outputs only the "real" atoms in an RMF file into the PDB it generates. For RMFs containing no atoms, it generates an empty PDB file. This is, of course, correct, but it should print a warning that no atoms were found. It should also be possible to translate other XYZ-type nodes into sort-of PDB entries - for example, the PDB files generated by IMP::pmi contain dummy atoms for each bead in the system.