[phenixbb] mmtbx.prepare_pdb_deposition sequence file

Ursula Schulze-Gahmen uschulze-gahmen at lbl.gov
Thu Nov 9 13:29:41 PST 2017

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):
line 99, in <module>
line 69, in run
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


Ursula Schulze-Gahmen, Ph.D.
Project Scientist
UC Berkeley, QB3
360 Stanley Hall #3220
Berkeley, CA 94720-3220
(510) 643 9491
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