I have problems running 'mmtbx.prepare_pdb_deposition' on the cif file created in phenix. I think the problem may be the sequence file. The coordinates are from a complex of 4 proteins plus an RNA. I created a text file with 5 chains, each chain sequence in one letter code. I am getting the following error code when I try to run the program: Traceback (most recent call last): File "/home/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/build/../modules/cctbx_project/mmtbx/command_line/prepare_pdb_deposition.py", line 99, in <module> run(sys.argv[1:]) File "/home/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/build/../modules/cctbx_project/mmtbx/command_line/prepare_pdb_deposition.py", line 69, in run alignment_params=params) File "/home/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/modules/cctbx_project/iotbx/pdb/hierarchy.py", line 1052, in as_cif_block_with_sequence assert len(chain.residue_groups) + chain.n_missing_start + chain.n_missing_end == len(sequence) There seems to be something wrong with chain N, but I am not sure what. Is it ok to have a longer sequence in the sequence file than in the coordinates? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491