Dear phenixbb, When I use phenix.sort_hetero_atoms to resort my pdb, there are duplicated residue number of water and aa in the output pdb. Is this a bug? As there are many number gaps water, how can I fix it? Best wishes! Lu -- 卢作焜 南开大学新生物站A202 Lu Zuokun, Ph.D. Candidate College of Life Science, Nankai University