Thank you Ben.

Effectively. T should be 7 but it is being numbered as 4. Even with dashes indicating 6 gaps before the T.

Sorry if I wasn't clear. By offset I ment the output positions not following my alignment.

Yup. the "..." in the sequence is just the rest of the sequence (to make the message shorter) :)

Best

Pedro

On Mon, Mar 1, 2021, 7:42 PM Modeller Caretaker <modeller-care@salilab.org> wrote:

On 2/28/21 1:00 PM, Pedro Guillem wrote:
> 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)

Dashes/gaps do not have any effect on which residues are read from the
PDB file; this is controlled entirely by the PIR header (the line
starting with "structureX", where you - apparently correctly - have 4 as
the start residue number). Dashes/gaps only control the correspondence
between target and template residues.

> Here is a bit of my ali file. I want the TRL of the template to align
> with the TRM of the sequence.

Your alignment looks fine to me, assuming by "..." you mean "the rest of
the sequence goes here". (A literal "." has a special meaning to
Modeller; read in the manual about modeling with ligands.)

> When it finishes, the position of TRM has a different offset in relation
> to TRL

Not sure what you mean here, unless you were expecting T to be numbered
4. Modeller numbers residues in your model starting from 1, regardless
of your alignment. If you want a different numbering, use
rename_segments(); see
https://salilab.org/modeller/10.0/manual/node23.html
and
https://salilab.org/modeller/10.0/manual/node30.html

        Ben Webb, Modeller Caretaker
--
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