Hello all,

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 TRL 

Am i doing something wrong here?

>P1;template
structureX:template:4:A:330:A:xxxxx:xxxxxxx:2.30:0.211
------TRL......................rest of seq*

>P1;seq
sequence:seq:.:.:.:.::::
EAARRRTRM........ rest of seq*

Thanks in advance.

Pedro