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 > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >