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