Hi,
I am trying to make a comparative model using modeler. I downloaded my sequence from uniprot and a homolog protein from the pdb. I associated the sequence with the homologe and the alignment is okay however there are definitely regions where there is no match at all. So when I run modeler it fails with the following output:
get_ran_648E> Alignment sequence does not match that in PDB file: 1 ./6opc_1.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).
I have been trying to figure out how exactly to specify the chain IDs and residue numbers but I really didn’t get it. May I ask you to provide an example please?
Best,
David