PTM "keep" mode

[AleksandraPanfilova]

"/groups/sbinlab/panf/PRISM/software/rosetta_ddG_pipeline/relax_parse_results.py", line 263, in <module> parse_relax_results(folder, sc_name=sys.argv[8], is_MP=is_MP, pdb_id=pdb_id, do_checking=do_checking) File "/groups/sbinlab/panf/PRISM/software/rosetta_ddG_pipeline/relax_parse_results.py", line 98, in parse_relax_results consistency = check_consitency(input_pdb, output_pdb, chain=chain, is_MP=is_MP, pdb_id=pdb_id) File "/groups/sbinlab/panf/PRISM/software/rosetta_ddG_pipeline/relax_parse_results.py", line 228, in check_consitency complete = check_seq_completeness(input_pdb, output_pdb) File "/groups/sbinlab/panf/PRISM/software/rosetta_ddG_pipeline/relax_parse_results.py", line 131, in check_seq_completeness seq2, seq2num, maxi2 = get_seq(input_pdb, isfile=True) File "/lustre/hpc/sbinlab/panf/PRISM/software/rosetta_ddG_pipeline/mp_helper.py", line 74, in get_seq seq[resseq-1] = d3to1[resname] KeyError: 'CGU'

1. Figure out why this error did not occur for the test case 1KNE
2. Fix.