> > No. As you discovered you'll lose information that way. I would just > align the two templates together and go from there.
But this means that the four domains for which I have the X-ray of my target would be moved a little and I want to avoid it. Can I tell modeller not to move them?
That won't work (as you saw) since the inifile has to have exactly the > same sequence as the final model.
Indeed I added the two missing domains (manually aligned with the template). In this way my infile has exactly the same residues present in the alignment file for the target sequence, but I expect modeller to refine only the two domains I manually add.
Thank you very much for your support,
Il giorno mar 25 feb 2020 alle ore 23:37 Modeller Caretaker < email@example.com> ha scritto:
> On 2/25/20 2:33 PM, Stefano Motta wrote: > > Thanks for your answer. Do you mean that I should remove the 4 domains > > present in the X-ray of my target protein from the homologous template? > > No. As you discovered you'll lose information that way. I would just > align the two templates together and go from there. > > > I thought a good idea would be to use as input > > model (inifile) the X-ray structure of my target protein > > That won't work (as you saw) since the inifile has to have exactly the > same sequence as the final model. > > Ben Webb, Modeller Caretaker > -- > firstname.lastname@example.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >