Re: [modeller_usage] Threading sequence onto template with missing residues

[Modeller Caretaker <>]

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
--
             https://salilab.org/modeller/
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