I have two sequences with low sequence identity and I get an alignment in
modeller different than clustalW, which also differs from when I use emboss
I also have a missing segment in my template, I want the final model to
have the corresponding segments and the gaps unmodeled, same as the
I tried to modify the alignment manually, however I ran into the
"SequenceMismatchError: read_te_291E> Sequence difference between alignment
and pdb :" error, which I think has to do with the number of residues in
the header of the alignment.
I attached the modeller and matcher alignments, in pir and fasta
respectively. I would appreciate if you tell me how to prevent the missing
loops in the template from being built and how to modify the alignment
manually bypassing the above error.
Also, do give your input regarding the difference in alignments, and how to
choose the most accurate one. I'm also fine with sharing the files