I'm trying to model from a known template (ident 37%).
The template is missing the first 3 residues in the structure.
- I start reading the template at position 4.
- I add 3 dashes to the beginning of the template to compensate for the
missing residues. (otherwise I get a "residue mismatch" error from modeller)
Now, my alignment needs 3 additional gaps at the start of the template.
No matter what I do, adding 6 dashes to the beginning of the template (3
for the missing residues and 3 extra for my alignment) has no effect on the
outcome and the model doesn't align with the template in the way I expect.
Here is a bit of my ali file. I want the TRL of the template to align with
the TRM of the sequence.
When it finishes, the position of TRM has a different offset in relation to
Am i doing something wrong here?
------TR*L*......................rest of seq*
EAARRRTR*M*........ rest of seq*
Thanks in advance.