On 5/4/20 6:56 AM, Ahmad Khalifa wrote: > I have a template with lots of missing residues. I want to thread my > target sequence onto the aligned parts of the template that are present > without moving my target structure in these areas.
This is the default Modeller behavior when constructing the initial model (*.ini file).
> In my target sequence, I also wish to know how to skip modeling the > missing parts altogether, thus making the job a mere threading of > aligned unknown regions onto the known ones.
To do that, override automodel.select_atoms as per https://salilab.org/modeller/9.24/manual/node23.html and select only the aligned residues. If you want to automate it, look at model.get_insertions() at https://salilab.org/modeller/9.24/manual/node176.html
Ben Webb, Modeller Caretaker