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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.
The text was updated successfully, but these errors were encountered:
When testing structure 6NCE I get a sequence match error from Modeller as follows:
And you could easily see that indeed the expected sequence is not the one reflected in the
.ali
file. As inEYRQNLIQALKKTPYHP/XXXXXXXXXXXXXXXX/XXXXXXXXXXXXXXXX*
from "custom" built.ali
file compared toEYRQNLIQALKKTP/tjtteelteeejeetl/ejettltttejtteel*
from the generated.seq
.The text was updated successfully, but these errors were encountered: