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
