On 9/2/19 4:00 PM, Ahmad Khalifa wrote: > 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 matcher.
This is unsurprising, since different algorithms are likely being used here to make these alignments.
> 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 > template.
If you don't want part of the sequence in the model, exclude it from your alignment. Modeller only models the sequence you give it. You may need to add a chain break (/ character) to the alignment to prevent Modeller from trying to connect the residues on either side of the gap with a peptide bond.
Ben Webb, Modeller Caretaker