When running modeller to model a sequence on a template pdb 4QTA
(obtained from BLAST, pdbaa database), I figured out that the sequence
of the pdb from blast output is different from the original pdb
sequence
BLAST works with the full primary amino acid sequence. Modeller is only
interested in the sequence for which there is structure in the PDB file
(ATOM records). If you look at the REMARK 465 records in the 4qta PDB
file you'll see that a number of residues at the N and C termini, plus a
few around residues 176-189, are missing in the PDB file.
_modeller.SequenceMismatchError: get_ran_648E> Alignment sequence does
not match that in PDB file: 1 ./4QTA.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).
...
May I please ask your comments and solution to how this problem can be
solved? , and please let me know why is this problem occurring?
Put residue numbers into your alignment file, as suggested by Modeller's
error message, and then it will show you where the two sequences diverge.