Support for protein+DNA structures

[ijpulidos]

When testing structure 6NCE I get a sequence match error from Modeller as follows:

Traceback (most recent call last):
  File "../complete_residues.py", line 219, in <module>
    complete_residues(code, align_file=args.output, loop_ref=args.loop_ref)
  File "../complete_residues.py", line 166, in complete_residues
    a.make()
  File "/home/mefisto/miniconda3/envs/mdcli-env/lib/python3.7/site-packages/modeller/automodel/automodel.py", line 139, in make
    self.homcsr(exit_stage)
  File "/home/mefisto/miniconda3/envs/mdcli-env/lib/python3.7/site-packages/modeller/automodel/automodel.py", line 602, in homcsr
    aln = self.read_alignment()
  File "/home/mefisto/miniconda3/envs/mdcli-env/lib/python3.7/site-packages/modeller/automodel/automodel.py", line 563, in read_alignment
    aln.append(file=self.alnfile, align_codes=codes)
  File "/home/mefisto/miniconda3/envs/mdcli-env/lib/python3.7/site-packages/modeller/alignment.py", line 78, in append
    allow_alternates)
_modeller.SequenceMismatchError: get_ran_648E> Alignment sequence does not match that in PDB file:        1  ./6nce.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one-letter code matches (e.g. B to N, Z to Q).

And you could easily see that indeed the expected sequence is not the one reflected in the .ali file. As in

EYRQNLIQALKKTPYHP/XXXXXXXXXXXXXXXX/XXXXXXXXXXXXXXXX* from "custom" built .ali file compared to EYRQNLIQALKKTP/tjtteelteeejeetl/ejettltttejtteel* from the generated .seq.