Hello all,
Any additional comments or suggestions on this issue? So far I have not been able to make modeller follow my alignment.
Is there an *explicit way *to tell modeller which residue (in the template) must be aligned with which residue in the sequence?
ie: align->template:1:21 to sequence:7:27
I'm looking to keep the structure identical in some segments.. and have modeller make a best guess in other parts.
Best Pedro
El lun, 1 mar 2021 a las 20:01, Pedro Guillem (pedro.guillem@gmail.com) escribió:
> 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 >> >